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+ + +
+ +
+
+
+ +
+
+
+
+ +
+

cases_by_location(location)

+
+
+outbreak_data.cases_by_location(location, server='api.outbreak.info', auth=None, pull_smoothed=0)
+

Loads data from a location if input is a string, or from multiple locations +if location is a list of string locations. Since this API endpoint supports paging, collect_all is used to return all data.

+
+
Arguments:
+
location:
+

A string or list of strings, separate multiple locations by “,”

+
+
pull_smoothed:
+

For every value >= 0, returns 1000 obs. (paging)

+
+
return:
+

A pandas dataframe

+
+
+
+
+
+ +

Example usage:

+
#Get the number of SARS-CoV-2 cases in Colorado.
+df = outbreak_data.cases_by_location('USA_US-CO')
+print(df)
+
+
+
+
Output:
+
                              _id    _score    admin1   confirmed_numIncrease  \
+ 0     USA_Colorado_None2021-03-14  8.438688  Colorado                    505
+ 1     USA_Colorado_None2021-03-18  8.438688  Colorado                   1060
+ 2     USA_Colorado_None2021-03-20  8.438688  Colorado                    852
+ 3     USA_Colorado_None2021-03-26  8.438688  Colorado                   1184
+ 4     USA_Colorado_None2021-04-07  8.438688  Colorado                   1897
+ ...                           ...       ...       ...                    ...
+ 1116  USA_Colorado_None2022-06-22  8.397695  Colorado                   2226
+ 1117  USA_Colorado_None2022-06-29  8.397695  Colorado                   2402
+ 1118  USA_Colorado_None2022-07-09  8.397695  Colorado                   1348
+ 1119  USA_Colorado_None2022-07-14  8.397695  Colorado                   1924
+ 1120  USA_Colorado_None2022-07-16  8.397695  Colorado                   1231
+
+             date
+ 0     2021-03-14
+ 1     2021-03-18
+ 2     2021-03-20
+ 3     2021-03-26
+ 4     2021-04-07
+ ...          ...
+ 1116  2022-06-22
+ 1117  2022-06-29
+ 1118  2022-07-09
+ 1119  2022-07-14
+ 1120  2022-07-16
+
+
+
+

[1121 rows x 5 columns]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Global_Prev.html b/Global_Prev.html new file mode 100644 index 0000000..04d3485 --- /dev/null +++ b/Global_Prev.html @@ -0,0 +1,309 @@ + + + + + + + + + + + global_prevalence(pango_lin, mutations, cumulative) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +
+ + + + + +
+
+ Join us on GitHub +
+ + +
+ + + + + + + + + + + + + + + + + + + +
+ +
    + +
  • »
    • + +
  • global_prevalence(pango_lin, mutations, cumulative)
    • + + +
  • + + + View page source + + +
    • + +
+ + +
+
+
+
+ +
+

global_prevalence(pango_lin, mutations, cumulative)

+
+
+outbreak_data.global_prevalence(pango_lin, mutations=None, cumulative=None, server='api.outbreak.info')
+

Returns the global daily prevalence of a PANGO lineage

+
+
Arguments:
+
param pangolin_lineage
+

(Required).

+
+
param mutations
+

(Somewhat optional). Comma separated list of mutations.

+
+
param cumulative
+

(Somewhat optional). If true returns the cumulative global prevalence since the first day of detection.

+
+
return
+

A pandas dataframe.

+
+
+
+
+
+ +

Example: Get global info on lineage ‘XBB’:

+
df = outbreak_data.global_prevalence('xbb')
+print(df)
+
+
+
+
Output:
+
            date  total_count  lineage_count  total_count_rolling  \
+ 0    2021-06-29        15453              2         10772.428571
+ 1    2021-06-30        13101              0         11060.571429
+ 2    2021-07-01        13088              0         11495.000000
+ 3    2021-07-02        11562              0         11890.571429
+ 4    2021-07-03         8310              0         11845.571429
+ ..          ...          ...            ...                  ...
+ 713  2023-06-12           27              0           112.428571
+ 714  2023-06-13            8              0            61.714286
+ 715  2023-06-14            1              0            36.000000
+ 716  2023-06-15            1              0            25.285714
+ 717  2023-06-17            1              0             8.000000
+
+      lineage_count_rolling  proportion  proportion_ci_lower  \
+ 0                 0.285714    0.000027         4.558329e-08
+ 1                 0.285714    0.000026         4.439232e-08
+ 2                 0.285714    0.000025         4.271630e-08
+ 3                 0.285714    0.000024         4.129377e-08
+ 4                 0.285714    0.000024         4.145063e-08
+ ..                     ...         ...                  ...
+ 713               0.142857    0.001271         4.374452e-06
+ 714               0.000000    0.000000         7.888011e-06
+ 715               0.000000    0.000000         1.354537e-05
+ 716               0.000000    0.000000         1.944577e-05
+ 717               0.000000    0.000000         5.949030e-05
+
+      proportion_ci_upper
+ 0               0.000233
+ 1               0.000227
+ 2               0.000218
+ 3               0.000211
+ 4               0.000212
+ ..                   ...
+ 713             0.022129
+ 714             0.039548
+ 715             0.066944
+ 716             0.094683
+ 717             0.262217
+
+
+
+

[718 rows x 8 columns]

+
+ + +
+ +
+ +
+
+ +
+ +
+ + + + + + + + + + + \ No newline at end of file diff --git a/Lineage_mutations.html b/Lineage_mutations.html new file mode 100644 index 0000000..3bb4590 --- /dev/null +++ b/Lineage_mutations.html @@ -0,0 +1,321 @@ + + + + + + + lineage_mutations(pango_lin, mutation, freq) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

lineage_mutations(pango_lin, mutation, freq)

+
+
+outbreak_data.lineage_mutations(pango_lin=None, lineage_crumbs=False, mutations=None, freq=0.8, server='api.outbreak.info', auth=None)
+

Retrieves data from all mutations in a specified lineage above a frequency threshold. +- Use ‘OR’ in a string to return overlapping mutations in multiple lineages: ‘BA.2 OR BA.1’

+
+
+
Arguments:
+
pango_lin:
+

A string; loads data for all mutations in a specified PANGO lineage

+
+
lineage_crumbs:
+

If true returns data for descendant lineages of pango_lin. Include the wildcard ‘*’ in string to return info on all related lineages.

+
+
mutations:
+

A string; loads mutation data for the specified sequence under the specified PANGO lineage

+
+
freq:
+

A number between 0 and 1 specifying the frequency threshold above which to return mutations (default = 0.8)

+
+
return:
+

A pandas dataframe

+
+
+
+
+
+
+ +

Example usage:

+
    +

  1. Get a list of all mutations and relevant data associated with the variant ‘B.1.1.7’:

    +
    df = outbreak_data.lineage_mutations('b.1.1.7')
+print(df)
+
    +
    +
    2. +
+
+
Output:
+
               mutation  mutation_count  lineage_count  lineage   gene  \
+ 0                n:d3l         1133368        1154337  b.1.1.7      N
+ 1              n:r203k         1131899        1154337  b.1.1.7      N
+ 2              s:d614g         1150796        1154337  b.1.1.7      S
+ 3         orf1a:t1001i         1149579        1154337  b.1.1.7  ORF1a
+ 4            orf8:s84l         1148665        1154337  b.1.1.7   ORF8
+ 5              s:a570d         1147678        1154337  b.1.1.7      S
+ 6              s:p681h         1147591        1154337  b.1.1.7      S
+ 7          orf1b:p314l         1147331        1154337  b.1.1.7  ORF1b
+ 8             s:d1118h         1147009        1154337  b.1.1.7      S
+ 9         orf1a:a1708d         1146288        1154337  b.1.1.7  ORF1a
+ 10           orf8:y73c         1144041        1154337  b.1.1.7   ORF8
+ 11             s:s982a         1142512        1154337  b.1.1.7      S
+ 12           orf8:q27*         1142465        1154337  b.1.1.7   ORF8
+ 13             s:t716i         1142087        1154337  b.1.1.7      S
+ 14             n:s235f         1141424        1154337  b.1.1.7      N
+ 15           orf8:r52i         1138388        1154337  b.1.1.7   ORF8
+ 16             s:n501y         1129018        1154337  b.1.1.7      S
+ 17        orf1a:i2230t         1127643        1154337  b.1.1.7  ORF1a
+ 18  orf1a:del3675/3677         1115708        1154337  b.1.1.7  ORF1a
+ 19          s:del69/70         1114288        1154337  b.1.1.7      S
+ 20        s:del144/144         1093432        1154337  b.1.1.7      S
+ 21             n:g204r         1050444        1154337  b.1.1.7      N
+
+                 ref_aa        alt_aa  codon_num codon_end          type  \
+ 0                    D             L          3      None  substitution
+ 1                    R             K        203      None  substitution
+ 2                    D             G        614      None  substitution
+ 3                    T             I       1001      None  substitution
+ 4                    S             L         84      None  substitution
+ 5                    A             D        570      None  substitution
+ 6                    P             H        681      None  substitution
+ 7                    P             L        314      None  substitution
+ 8                    D             H       1118      None  substitution
+ 9                    A             D       1708      None  substitution
+ 10                   Y             C         73      None  substitution
+ 11                   S             A        982      None  substitution
+ 12                   Q             *         27      None  substitution
+ 13                   T             I        716      None  substitution
+ 14                   S             F        235      None  substitution
+ 15                   R             I         52      None  substitution
+ 16                   N             Y        501      None  substitution
+ 17                   I             T       2230      None  substitution
+ 18  ORF1A:DEL3675/3677  DEL3675/3677       3675    3677.0      deletion
+ 19          S:DEL69/70      DEL69/70         69      70.0      deletion
+ 20        S:DEL144/144    DEL144/144        144     144.0      deletion
+ 21                   G             R        204      None  substitution
+
+     prevalence change_length_nt
+ 0     0.981835             None
+ 1     0.980562             None
+ 2     0.996932             None
+ 3     0.995878             None
+ 4     0.995086             None
+ 5     0.994231             None
+ 6     0.994156             None
+ 7     0.993931             None
+ 8     0.993652             None
+ 9     0.993027             None
+ 10    0.991081             None
+ 11    0.989756             None
+ 12    0.989715             None
+ 13    0.989388             None
+ 14    0.988813             None
+ 15    0.986183             None
+ 16    0.978066             None
+ 17    0.976875             None
+ 18    0.966536              9.0
+ 19    0.965306              6.0
+ 20    0.947238              3.0
+ 21    0.909998             None
+
+
+
+
    +

  1. Mutiple queries for lineages and mutations can be separated by “,”:

    +
    #Find mutation information for B.1.1.7, P.1, and XBB.1.5
+df = outbreak_data_lineage_mutations('b.1.1.7, p.1, xbb.1.5')
+print(df)
+
    +
    +
    2. +
+
+
Output
+
         mutation  mutation_count  lineage_count  lineage   gene        ref_aa  \
+ 0          n:d3l         1133368        1154337  b.1.1.7      N             D
+ 1        n:r203k         1131899        1154337  b.1.1.7      N             R
+ 2        s:d614g         1150796        1154337  b.1.1.7      S             D
+ 3   orf1a:t1001i         1149579        1154337  b.1.1.7  ORF1a             T
+ 4      orf8:s84l         1148665        1154337  b.1.1.7   ORF8             S
+ ..           ...             ...            ...      ...    ...           ...
+ 63       s:g446s          156244         167128  xbb.1.5      S             G
+ 64  s:del144/144          154766         167128  xbb.1.5      S  S:DEL144/144
+ 65       s:h146q          153308         167128  xbb.1.5      S             H
+ 66       s:r408s          152365         167128  xbb.1.5      S             R
+ 67       s:k417n          147604         167128  xbb.1.5      S             K
+
+         alt_aa  codon_num codon_end          type  prevalence change_length_nt
+ 0            L          3      None  substitution    0.981835             None
+ 1            K        203      None  substitution    0.980562             None
+ 2            G        614      None  substitution    0.996932             None
+ 3            I       1001      None  substitution    0.995878             None
+ 4            L         84      None  substitution    0.995086             None
+ ..         ...        ...       ...           ...         ...              ...
+ 63           S        446      None  substitution    0.934876             None
+ 64  DEL144/144        144     144.0      deletion    0.926033              3.0
+ 65           Q        146      None  substitution    0.917309             None
+ 66           S        408      None  substitution    0.911667             None
+ 67           N        417      None  substitution    0.883179             None
+
+
+
+

[113 rows x 12 columns]

+
    +

  1. Use ‘OR’ in a string to return overlapping mutations in multiple lineages:

    +
    df = outbreak_data.lineage_mutations('ba.2 OR xbb.1.5')
+print(df)
+
    +
    +
    2. +
+
+
Output
+
              mutation  mutation_count  lineage_count         lineage   gene  \
+ 0             n:r203k          237984         243206  P.1 OR xbb.1.5      N
+ 1             s:d614g          242522         243206  P.1 OR xbb.1.5      S
+ 2         orf1b:p314l          242226         243206  P.1 OR xbb.1.5  ORF1b
+ 3             s:h655y          241765         243206  P.1 OR xbb.1.5      S
+ 4           orf8:s84l          240116         243206  P.1 OR xbb.1.5   ORF8
+ 5             n:g204r          238101         243206  P.1 OR xbb.1.5      N
+ 6             s:n501y          235654         243206  P.1 OR xbb.1.5      S
+ 7  orf1a:del3675/3677          226006         243206  P.1 OR xbb.1.5  ORF1a
+
+                ref_aa        alt_aa  codon_num codon_end          type  \
+ 0                   R             K        203      None  substitution
+ 1                   D             G        614      None  substitution
+ 2                   P             L        314      None  substitution
+ 3                   H             Y        655      None  substitution
+ 4                   S             L         84      None  substitution
+ 5                   G             R        204      None  substitution
+ 6                   N             Y        501      None  substitution
+ 7  ORF1A:DEL3675/3677  DEL3675/3677       3675    3677.0      deletion
+
+    prevalence change_length_nt
+ 0    0.978528             None
+ 1    0.997188             None
+ 2    0.995970             None
+ 3    0.994075             None
+ 4    0.987295             None
+ 5    0.979010             None
+ 6    0.968948             None
+ 7    0.929278              9.0
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Mut_By_Lin.html b/Mut_By_Lin.html new file mode 100644 index 0000000..d16e407 --- /dev/null +++ b/Mut_By_Lin.html @@ -0,0 +1,306 @@ + + + + + + + + + + + mutations_by_lineage(mutation, location, pango_lin) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +
+ + + + + +
+
+ Join us on GitHub +
+ + +
+ + + + + + + + + + + + + + + + + + + +
+ +
    + +
  • »
    • + +
  • mutations_by_lineage(mutation, location, pango_lin)
    • + + +
  • + + + View page source + + +
    • + +
+ + +
+
+
+
+ +
+

mutations_by_lineage(mutation, location, pango_lin)

+
+
+outbreak_data.mutations_by_lineage(mutation=None, location=None, pango_lin=None, lineage_crumbs=False, datemin=None, datemax=None, freq=None, server='api.outbreak.info')
+

Returns the prevalence of a mutation or series of mutations across specified lineages by location

+
+
Arguments:
+
param mutations
+

(Optional). List or string of mutations separated by “,”.

+
+
param location_id
+

(Optional). A string; If not specified, return most recent date globally.

+
+
param pangolin_lineage
+

(Optional). If not specfied, returns all Pango lineages containing that mutation.

+
+
param frequency
+

(Optional) Minimimum frequency threshold for the prevalence of a mutation in a lineage.

+
+
param datemin
+

(Optional). A string representing the first cutoff date for returned date. Must be in YYYY-MM-DD format and be before ‘datemax’

+
+
param datemax
+

(Optional). A string representing the second cutoff date. Must be in YYY-MM-DD format and be after ‘datemin’

+
+
return
+

A pandas dataframe.

+
+
+
+
+
+ +

Example usage:

+
#Get info on mutation 'orf1b:p314l'
+df = od.mutations_by_lineage('orf1b:p314l')
+print(df)
+
+
+
+
Output
+
         pangolin_lineage  lineage_count  mutation_count  proportion  \
+ 0                   ba.2        1227503         1222717    0.996101
+ 1                b.1.1.7        1154337         1147331    0.993931
+ 2                 ba.1.1        1044480         1039813    0.995532
+ 3                   ay.4         858839          854935    0.995454
+ 4                   ba.1         438947          437207    0.996036
+ ...                  ...            ...             ...         ...
+ 2851                fn.1              1               1    1.000000
+ 2852  miscba1ba2post5386              1               1    1.000000
+ 2853            xbb.1.23              1               1    1.000000
+ 2854            xbb.1.37              1               1    1.000000
+ 2855                 xbv              1               1    1.000000
+
+       proportion_ci_lower  proportion_ci_upper
+ 0                0.995990             0.996210
+ 1                0.993788             0.994071
+ 2                0.995402             0.995658
+ 3                0.995310             0.995595
+ 4                0.995847             0.996219
+ ...                   ...                  ...
+ 2851             0.146746             0.999614
+ 2852             0.146746             0.999614
+ 2853             0.146746             0.999614
+ 2854             0.146746             0.999614
+ 2855             0.146746             0.999614
+
+
+
+

[2856 rows x 6 columns]

+
+ + +
+ +
+ +
+
+ +
+ +
+ + + + + + + + + + + \ No newline at end of file diff --git a/Outbreak_data_Functions.html b/Outbreak_data_Functions.html new file mode 100644 index 0000000..9c7452d --- /dev/null +++ b/Outbreak_data_Functions.html @@ -0,0 +1,169 @@ + + + + + + + get_outbreak_data() — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

get_outbreak_data()

+
+

Note

+

This is a hidden function.

+
+
+
+outbreak_data.get_outbreak_data(endpoint, argstring, server='api.outbreak.info', auth=None, collect_all=False, curr_page=0)
+

Receives raw data using outbreak API.

+
+
Arguments:
+
endpoint:
+

directory in server the data is stored

+
+
argstring:
+

feature arguments to provide to API call

+
+
server:
+

Server to request from

+
+
auth:
+

Auth key (defaults to acceptable state)

+
+
collect_all:
+

if True, returns all data.

+
+
curr_page:
+

iterator state for paging

+
+
return:
+

A request object containing the raw data

+
+
+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Prevalence_by_location.html b/Prevalence_by_location.html new file mode 100644 index 0000000..7b0613d --- /dev/null +++ b/Prevalence_by_location.html @@ -0,0 +1,228 @@ + + + + + + + prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None)
    • +
  • + View page source +
    • +
+
+
+
+
+ +
+

prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None)

+
+
+outbreak_data.prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None, server='api.outbreak.info')
+

Returns the daily prevalence of a PANGO lineage by location.

+
+
Arguments:
+
pango_lin:
+

(Required). List of lineages separated by ,

+
+
location_id:
+

(Optional). Default location: USA

+
+
mutations:
+

(Optional). List of mutations separated by AND

+
+
cumulative:
+

(Optional). If true returns the cumulative global prevalence since the first day of detection.

+
+
datemin:
+

(Optional). A string representing the first cutoff date for returned date. Must be in YYYY-MM-DD format and be before ‘datemax’

+
+
datemax:
+

(Optional). A string representing the second cutoff date. Must be in YYY-MM-DD format and be after ‘datemin’

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +

Example usage:

+
    +

  1. Get the daily prevalence of lineage ‘BA.2’ in India since first detection:

    +
    df1 = od.daily_prev('ba.2', "IND")
+print(df1)
+
    +
    +
    2. +
+
+
Output
+
             date  total_count  lineage_count  total_count_rolling  \
+ 0     2020-08-01           39              1            29.000000
+ 1     2020-08-02          100              0            41.285714
+ 2     2020-08-03           38              0            42.000000
+ 3     2020-08-04           20              0            42.285714
+ 4     2020-08-05           26              0            36.000000
+ ...          ...          ...            ...                  ...
+ 1017  2023-05-15            2              0             5.857143
+ 1018  2023-05-16            3              0             5.142857
+ 1019  2023-05-17            3              0             3.285714
+ 1020  2023-05-18            2              0             3.142857
+ 1021  2023-05-20            1              0             2.000000
+
+       lineage_count_rolling  proportion  proportion_ci_lower  \
+ 0                  0.142857    0.004926             0.000017
+ 1                  0.142857    0.003460             0.000012
+ 2                  0.142857    0.003401             0.000012
+ 3                  0.142857    0.003378             0.000012
+ 4                  0.142857    0.003968             0.000014
+ ...                     ...         ...                  ...
+ 1017               0.000000    0.000000             0.000078
+ 1018               0.000000    0.000000             0.000093
+ 1019               0.000000    0.000000             0.000151
+ 1020               0.000000    0.000000             0.000151
+ 1021               0.000000    0.000000             0.000217
+
+       proportion_ci_upper
+ 0                0.082286
+ 1                0.059076
+ 2                0.057719
+ 3                0.057719
+ 4                0.066944
+ ...                   ...
+ 1017             0.330389
+ 1018             0.379377
+ 1019             0.535583
+ 1020             0.535583
+ 1021             0.666822
+
+
+
+
    +

  1. Get a cumulative summary of information regarding ‘BA.2’ in India:

    +
    df2 = od.daily_prev('ba.2', "IND", cumulative = True)
+print(df2)
+
    +
    +
    2. +
+
+
Output
+
                        Values
+ first_detected     2020-08-01
+ global_prevalence    0.109641
+ last_detected      2023-04-26
+ lineage_count           25561
+ total_count            233134
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/Seq_counts.html b/Seq_counts.html new file mode 100644 index 0000000..e06ecbf --- /dev/null +++ b/Seq_counts.html @@ -0,0 +1,188 @@ + + + + + + + sequence_counts(location, cumulative, sub_admin) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

sequence_counts(location, cumulative, sub_admin)

+
+
+outbreak_data.sequence_counts(location=None, cumulative=None, sub_admin=None, server='api.outbreak.info')
+

Returns number of sequences per day by location

+
+
Arguments:
+
location:
+

(Optional). If not specified, the global total counts are returned.

+
+
cumulative:
+

(Optional). If true returns the cumulative number of sequences till date.

+
+
subadmin:
+

(Optional). If true and cumulative=true, returns the cumulative number of sequences for the immedaite lower admin level.

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +

Example usage:

+
    +

  1. Get number of daily sequence counts in the US:

    +
    df = od.sequence_counts('USA')
+print(df)
+
    +
    +
    2. +
+
+
Output
+
            Key        Values
+ 0       mutation   ORF1b:P314L
+ 1      alt_codon           CTT
+ 2  is_synonymous         False
+ 3      codon_num           314
+ 4      ref_codon           CCT
+ 5           gene         ORF1b
+ 6            pos         14407
+ 7         alt_aa             L
+ 8         ref_aa             P
+ 9           type  substitution
+
+
+
+
    +

  1. Get total number of sequence counts

    +
    +

    df = od.sequence_counts(‘USA’, cumulative=True) +print(df)

    +
    +
    2. +
+
+
Output
+
               Values
+ total_count  4617418
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/_images/ca_cases.png b/_images/ca_cases.png new file mode 100644 index 0000000..9b53ced Binary files /dev/null and b/_images/ca_cases.png differ diff --git a/_images/compare.png b/_images/compare.png new file mode 100644 index 0000000..e615d9b Binary files /dev/null and b/_images/compare.png differ diff --git a/_images/multi_state_cases.png b/_images/multi_state_cases.png new file mode 100644 index 0000000..3d9a8ce Binary files /dev/null and b/_images/multi_state_cases.png differ diff --git a/_images/mut_by_lin.png b/_images/mut_by_lin.png new file mode 100644 index 0000000..1489409 Binary files /dev/null and b/_images/mut_by_lin.png differ diff --git a/_images/prev_visual.png b/_images/prev_visual.png new file mode 100644 index 0000000..3ebf535 Binary files /dev/null and b/_images/prev_visual.png differ diff --git a/_images/top4.png b/_images/top4.png new file mode 100644 index 0000000..12b7f1a Binary files /dev/null and b/_images/top4.png differ diff --git a/_sources/Cases_by_location.rst.txt b/_sources/Cases_by_location.rst.txt new file mode 100644 index 0000000..87d12ef --- /dev/null +++ b/_sources/Cases_by_location.rst.txt @@ -0,0 +1,41 @@ +cases_by_location(location) +----------------------------------- + +.. autofunction:: outbreak_data.cases_by_location + +Example usage:: + + #Get the number of SARS-CoV-2 cases in Colorado. + df = outbreak_data.cases_by_location('USA_US-CO') + print(df) + +.. code-block:: + :caption: Output: + + _id _score admin1 confirmed_numIncrease \ + 0 USA_Colorado_None2021-03-14 8.438688 Colorado 505 + 1 USA_Colorado_None2021-03-18 8.438688 Colorado 1060 + 2 USA_Colorado_None2021-03-20 8.438688 Colorado 852 + 3 USA_Colorado_None2021-03-26 8.438688 Colorado 1184 + 4 USA_Colorado_None2021-04-07 8.438688 Colorado 1897 + ... ... ... ... ... + 1116 USA_Colorado_None2022-06-22 8.397695 Colorado 2226 + 1117 USA_Colorado_None2022-06-29 8.397695 Colorado 2402 + 1118 USA_Colorado_None2022-07-09 8.397695 Colorado 1348 + 1119 USA_Colorado_None2022-07-14 8.397695 Colorado 1924 + 1120 USA_Colorado_None2022-07-16 8.397695 Colorado 1231 + + date + 0 2021-03-14 + 1 2021-03-18 + 2 2021-03-20 + 3 2021-03-26 + 4 2021-04-07 + ... ... + 1116 2022-06-22 + 1117 2022-06-29 + 1118 2022-07-09 + 1119 2022-07-14 + 1120 2022-07-16 + +[1121 rows x 5 columns] diff --git a/_sources/Global_Prev.rst.txt b/_sources/Global_Prev.rst.txt new file mode 100644 index 0000000..0fb8c7d --- /dev/null +++ b/_sources/Global_Prev.rst.txt @@ -0,0 +1,55 @@ +global_prevalence(pango_lin, mutations, cumulative) +---------------------------------------------------- + +.. autofunction:: outbreak_data.global_prevalence + +Example: Get global info on lineage 'XBB':: + + df = outbreak_data.global_prevalence('xbb') + print(df) + +.. code-block:: + :caption: Output: + + date total_count lineage_count total_count_rolling \ + 0 2021-06-29 15453 2 10772.428571 + 1 2021-06-30 13101 0 11060.571429 + 2 2021-07-01 13088 0 11495.000000 + 3 2021-07-02 11562 0 11890.571429 + 4 2021-07-03 8310 0 11845.571429 + .. ... ... ... ... + 713 2023-06-12 27 0 112.428571 + 714 2023-06-13 8 0 61.714286 + 715 2023-06-14 1 0 36.000000 + 716 2023-06-15 1 0 25.285714 + 717 2023-06-17 1 0 8.000000 + + lineage_count_rolling proportion proportion_ci_lower \ + 0 0.285714 0.000027 4.558329e-08 + 1 0.285714 0.000026 4.439232e-08 + 2 0.285714 0.000025 4.271630e-08 + 3 0.285714 0.000024 4.129377e-08 + 4 0.285714 0.000024 4.145063e-08 + .. ... ... ... + 713 0.142857 0.001271 4.374452e-06 + 714 0.000000 0.000000 7.888011e-06 + 715 0.000000 0.000000 1.354537e-05 + 716 0.000000 0.000000 1.944577e-05 + 717 0.000000 0.000000 5.949030e-05 + + proportion_ci_upper + 0 0.000233 + 1 0.000227 + 2 0.000218 + 3 0.000211 + 4 0.000212 + .. ... + 713 0.022129 + 714 0.039548 + 715 0.066944 + 716 0.094683 + 717 0.262217 + +[718 rows x 8 columns] + + diff --git a/_sources/Lineage_mutations.rst.txt b/_sources/Lineage_mutations.rst.txt new file mode 100644 index 0000000..b8a62de --- /dev/null +++ b/_sources/Lineage_mutations.rst.txt @@ -0,0 +1,163 @@ +lineage_mutations(pango_lin, mutation, freq) +-------------------------------------------- + +.. autofunction:: outbreak_data.lineage_mutations + +Example usage: + +1. Get a list of all mutations and relevant data associated with the variant 'B.1.1.7':: + + df = outbreak_data.lineage_mutations('b.1.1.7') + print(df) + +.. code-block:: + :caption: Output: + + mutation mutation_count lineage_count lineage gene \ + 0 n:d3l 1133368 1154337 b.1.1.7 N + 1 n:r203k 1131899 1154337 b.1.1.7 N + 2 s:d614g 1150796 1154337 b.1.1.7 S + 3 orf1a:t1001i 1149579 1154337 b.1.1.7 ORF1a + 4 orf8:s84l 1148665 1154337 b.1.1.7 ORF8 + 5 s:a570d 1147678 1154337 b.1.1.7 S + 6 s:p681h 1147591 1154337 b.1.1.7 S + 7 orf1b:p314l 1147331 1154337 b.1.1.7 ORF1b + 8 s:d1118h 1147009 1154337 b.1.1.7 S + 9 orf1a:a1708d 1146288 1154337 b.1.1.7 ORF1a + 10 orf8:y73c 1144041 1154337 b.1.1.7 ORF8 + 11 s:s982a 1142512 1154337 b.1.1.7 S + 12 orf8:q27* 1142465 1154337 b.1.1.7 ORF8 + 13 s:t716i 1142087 1154337 b.1.1.7 S + 14 n:s235f 1141424 1154337 b.1.1.7 N + 15 orf8:r52i 1138388 1154337 b.1.1.7 ORF8 + 16 s:n501y 1129018 1154337 b.1.1.7 S + 17 orf1a:i2230t 1127643 1154337 b.1.1.7 ORF1a + 18 orf1a:del3675/3677 1115708 1154337 b.1.1.7 ORF1a + 19 s:del69/70 1114288 1154337 b.1.1.7 S + 20 s:del144/144 1093432 1154337 b.1.1.7 S + 21 n:g204r 1050444 1154337 b.1.1.7 N + + ref_aa alt_aa codon_num codon_end type \ + 0 D L 3 None substitution + 1 R K 203 None substitution + 2 D G 614 None substitution + 3 T I 1001 None substitution + 4 S L 84 None substitution + 5 A D 570 None substitution + 6 P H 681 None substitution + 7 P L 314 None substitution + 8 D H 1118 None substitution + 9 A D 1708 None substitution + 10 Y C 73 None substitution + 11 S A 982 None substitution + 12 Q * 27 None substitution + 13 T I 716 None substitution + 14 S F 235 None substitution + 15 R I 52 None substitution + 16 N Y 501 None substitution + 17 I T 2230 None substitution + 18 ORF1A:DEL3675/3677 DEL3675/3677 3675 3677.0 deletion + 19 S:DEL69/70 DEL69/70 69 70.0 deletion + 20 S:DEL144/144 DEL144/144 144 144.0 deletion + 21 G R 204 None substitution + + prevalence change_length_nt + 0 0.981835 None + 1 0.980562 None + 2 0.996932 None + 3 0.995878 None + 4 0.995086 None + 5 0.994231 None + 6 0.994156 None + 7 0.993931 None + 8 0.993652 None + 9 0.993027 None + 10 0.991081 None + 11 0.989756 None + 12 0.989715 None + 13 0.989388 None + 14 0.988813 None + 15 0.986183 None + 16 0.978066 None + 17 0.976875 None + 18 0.966536 9.0 + 19 0.965306 6.0 + 20 0.947238 3.0 + 21 0.909998 None + +2. Mutiple queries for lineages and mutations can be separated by ",":: + + #Find mutation information for B.1.1.7, P.1, and XBB.1.5 + df = outbreak_data_lineage_mutations('b.1.1.7, p.1, xbb.1.5') + print(df) + +.. code-block:: + :caption: Output + + mutation mutation_count lineage_count lineage gene ref_aa \ + 0 n:d3l 1133368 1154337 b.1.1.7 N D + 1 n:r203k 1131899 1154337 b.1.1.7 N R + 2 s:d614g 1150796 1154337 b.1.1.7 S D + 3 orf1a:t1001i 1149579 1154337 b.1.1.7 ORF1a T + 4 orf8:s84l 1148665 1154337 b.1.1.7 ORF8 S + .. ... ... ... ... ... ... + 63 s:g446s 156244 167128 xbb.1.5 S G + 64 s:del144/144 154766 167128 xbb.1.5 S S:DEL144/144 + 65 s:h146q 153308 167128 xbb.1.5 S H + 66 s:r408s 152365 167128 xbb.1.5 S R + 67 s:k417n 147604 167128 xbb.1.5 S K + + alt_aa codon_num codon_end type prevalence change_length_nt + 0 L 3 None substitution 0.981835 None + 1 K 203 None substitution 0.980562 None + 2 G 614 None substitution 0.996932 None + 3 I 1001 None substitution 0.995878 None + 4 L 84 None substitution 0.995086 None + .. ... ... ... ... ... ... + 63 S 446 None substitution 0.934876 None + 64 DEL144/144 144 144.0 deletion 0.926033 3.0 + 65 Q 146 None substitution 0.917309 None + 66 S 408 None substitution 0.911667 None + 67 N 417 None substitution 0.883179 None + +[113 rows x 12 columns] + +3. Use 'OR' in a string to return overlapping mutations in multiple lineages:: + + df = outbreak_data.lineage_mutations('ba.2 OR xbb.1.5') + print(df) + +.. code-block:: + :caption: Output + + mutation mutation_count lineage_count lineage gene \ + 0 n:r203k 237984 243206 P.1 OR xbb.1.5 N + 1 s:d614g 242522 243206 P.1 OR xbb.1.5 S + 2 orf1b:p314l 242226 243206 P.1 OR xbb.1.5 ORF1b + 3 s:h655y 241765 243206 P.1 OR xbb.1.5 S + 4 orf8:s84l 240116 243206 P.1 OR xbb.1.5 ORF8 + 5 n:g204r 238101 243206 P.1 OR xbb.1.5 N + 6 s:n501y 235654 243206 P.1 OR xbb.1.5 S + 7 orf1a:del3675/3677 226006 243206 P.1 OR xbb.1.5 ORF1a + + ref_aa alt_aa codon_num codon_end type \ + 0 R K 203 None substitution + 1 D G 614 None substitution + 2 P L 314 None substitution + 3 H Y 655 None substitution + 4 S L 84 None substitution + 5 G R 204 None substitution + 6 N Y 501 None substitution + 7 ORF1A:DEL3675/3677 DEL3675/3677 3675 3677.0 deletion + + prevalence change_length_nt + 0 0.978528 None + 1 0.997188 None + 2 0.995970 None + 3 0.994075 None + 4 0.987295 None + 5 0.979010 None + 6 0.968948 None + 7 0.929278 9.0 + + diff --git a/_sources/Mut_By_Lin.rst.txt b/_sources/Mut_By_Lin.rst.txt new file mode 100644 index 0000000..704e94d --- /dev/null +++ b/_sources/Mut_By_Lin.rst.txt @@ -0,0 +1,44 @@ +mutations_by_lineage(mutation, location, pango_lin) +--------------------------------------------------- + +.. autofunction:: outbreak_data.mutations_by_lineage + + +Example usage:: + + #Get info on mutation 'orf1b:p314l' + df = od.mutations_by_lineage('orf1b:p314l') + print(df) + +.. code-block:: + :caption: Output + + pangolin_lineage lineage_count mutation_count proportion \ + 0 ba.2 1227503 1222717 0.996101 + 1 b.1.1.7 1154337 1147331 0.993931 + 2 ba.1.1 1044480 1039813 0.995532 + 3 ay.4 858839 854935 0.995454 + 4 ba.1 438947 437207 0.996036 + ... ... ... ... ... + 2851 fn.1 1 1 1.000000 + 2852 miscba1ba2post5386 1 1 1.000000 + 2853 xbb.1.23 1 1 1.000000 + 2854 xbb.1.37 1 1 1.000000 + 2855 xbv 1 1 1.000000 + + proportion_ci_lower proportion_ci_upper + 0 0.995990 0.996210 + 1 0.993788 0.994071 + 2 0.995402 0.995658 + 3 0.995310 0.995595 + 4 0.995847 0.996219 + ... ... ... + 2851 0.146746 0.999614 + 2852 0.146746 0.999614 + 2853 0.146746 0.999614 + 2854 0.146746 0.999614 + 2855 0.146746 0.999614 + +[2856 rows x 6 columns] + + diff --git a/_sources/Outbreak_data_Functions.rst.txt b/_sources/Outbreak_data_Functions.rst.txt new file mode 100644 index 0000000..fe550d8 --- /dev/null +++ b/_sources/Outbreak_data_Functions.rst.txt @@ -0,0 +1,15 @@ +get_outbreak_data() +--------------------------------- +.. note:: + + This is a hidden function. + + +.. autofunction:: outbreak_data.get_outbreak_data + + + + + + + diff --git a/_sources/Prevalence_by_location.rst.txt b/_sources/Prevalence_by_location.rst.txt new file mode 100644 index 0000000..17073e0 --- /dev/null +++ b/_sources/Prevalence_by_location.rst.txt @@ -0,0 +1,69 @@ +prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None) +--------------------------------------------------------------------------------------------------------- + +.. autofunction:: outbreak_data.prevalence_by_location + +Example usage: + +1. Get the daily prevalence of lineage 'BA.2' in India since first detection:: + + df1 = od.daily_prev('ba.2', "IND") + print(df1) + +.. code-block:: + :caption: Output + + date total_count lineage_count total_count_rolling \ + 0 2020-08-01 39 1 29.000000 + 1 2020-08-02 100 0 41.285714 + 2 2020-08-03 38 0 42.000000 + 3 2020-08-04 20 0 42.285714 + 4 2020-08-05 26 0 36.000000 + ... ... ... ... ... + 1017 2023-05-15 2 0 5.857143 + 1018 2023-05-16 3 0 5.142857 + 1019 2023-05-17 3 0 3.285714 + 1020 2023-05-18 2 0 3.142857 + 1021 2023-05-20 1 0 2.000000 + + lineage_count_rolling proportion proportion_ci_lower \ + 0 0.142857 0.004926 0.000017 + 1 0.142857 0.003460 0.000012 + 2 0.142857 0.003401 0.000012 + 3 0.142857 0.003378 0.000012 + 4 0.142857 0.003968 0.000014 + ... ... ... ... + 1017 0.000000 0.000000 0.000078 + 1018 0.000000 0.000000 0.000093 + 1019 0.000000 0.000000 0.000151 + 1020 0.000000 0.000000 0.000151 + 1021 0.000000 0.000000 0.000217 + + proportion_ci_upper + 0 0.082286 + 1 0.059076 + 2 0.057719 + 3 0.057719 + 4 0.066944 + ... ... + 1017 0.330389 + 1018 0.379377 + 1019 0.535583 + 1020 0.535583 + 1021 0.666822 + +2. Get a cumulative summary of information regarding 'BA.2' in India:: + + df2 = od.daily_prev('ba.2', "IND", cumulative = True) + print(df2) + +.. code-block:: + :caption: Output + + Values + first_detected 2020-08-01 + global_prevalence 0.109641 + last_detected 2023-04-26 + lineage_count 25561 + total_count 233134 + diff --git a/_sources/Seq_counts.rst.txt b/_sources/Seq_counts.rst.txt new file mode 100644 index 0000000..91764de --- /dev/null +++ b/_sources/Seq_counts.rst.txt @@ -0,0 +1,40 @@ +sequence_counts(location, cumulative, sub_admin) +------------------------------------------------- + +.. autofunction:: outbreak_data.sequence_counts + +Example usage: + +1. Get number of daily sequence counts in the US:: + + df = od.sequence_counts('USA') + print(df) + + +.. code-block:: + :caption: Output + + Key Values + 0 mutation ORF1b:P314L + 1 alt_codon CTT + 2 is_synonymous False + 3 codon_num 314 + 4 ref_codon CCT + 5 gene ORF1b + 6 pos 14407 + 7 alt_aa L + 8 ref_aa P + 9 type substitution + +2. Get total number of sequence counts + + df = od.sequence_counts('USA', cumulative=True) + print(df) + +.. code-block:: + :caption: Output + + Values + total_count 4617418 + + diff --git a/_sources/Workflows1.rst.txt b/_sources/Workflows1.rst.txt new file mode 100644 index 0000000..99926fa --- /dev/null +++ b/_sources/Workflows1.rst.txt @@ -0,0 +1,106 @@ + +Lineage and Mutation Analysis +----------------------------- + +Here is an example workflow that allows the user to manipulate the data to find all the XBB lineages prevalent in India within a 1-year timeframe:: + + import outbreak_data as od + import pandas as pd + + # Get the prevalence of all circulating XBB lineages in India + data = od.prevalence_by_location("IND", startswith = 'xbb') + # multiply prevalence values by 100% for scale + data['prevalence_rolling'] = data['prevalence_rolling'].apply(lambda x: x*100) + # Search for data based on date range + data = data.sort_values(by="date") + data = data.loc[data["date"].between("2020-09-12", "2022-03-31")] + + +.. code-block:: + :caption: Output: + + date total_count lineage_count lineage prevalence \ + 3014 2022-09-12 0 0 xbb.1.16 0.000000 + 3781 2022-09-12 0 0 xbb.2.3 0.000000 + 2593 2022-09-12 152 2 xbb.1 0.013158 + 3782 2022-09-13 0 0 xbb.2.3 0.000000 + 3015 2022-09-13 0 0 xbb.1.16 0.000000 + ... ... ... ... ... ... + 4086 2023-03-31 196 2 xbb.2.3.2 0.010204 + 3322 2023-03-31 196 29 xbb.1.16.1 0.147959 + 2793 2023-03-31 196 1 xbb.1 0.005102 + 3381 2023-03-31 196 7 xbb.1.16.2 0.035714 + 3981 2023-03-31 196 15 xbb.2.3 0.076531 + + prevalence_rolling + 3014 0.000000 + 3781 0.000000 + 2593 0.003451 + 3782 0.000000 + 3015 0.000000 + ... ... + 4086 0.031184 + 3322 0.144578 + 2793 0.014174 + 3381 0.045358 + 3981 0.084337 + +[985 rows x 6 columns] + +.. image:: prev_visual.* + +.. note:: The `Vega-Altair `_ visualization package is used for demonstration purposes. However, any Python visual package can be used to create graphi cal representations of the data. + +# Finding the Most Prevalent Lineages +If we wanted to determine and plot the top four most prevalent lineages in India, we can make a few queries and use a few simple commands to create a table that shows us what these lineages are:: + + data=od.prevalence_by_location("IND") + most_prev = data.groupby('lineage').apply(max) # Finds the lineages with the most hits + most_prev = most_prev.mask(most_prev == '').dropna(how = 'any') # Drop any unknowns + most_prev = most_prev.iloc[:4] + print(most_prev) + +.. code-block:: + :caption: Output + + date total_count lineage_count lineage prevalence \ + lineage + ba.2 2023-04-20 5668 1445 ba.2 0.822785 + ba.2.10.1 2023-04-19 5668 93 ba.2.10.1 0.285714 + bq.1.1 2023-03-27 402 7 bq.1.1 0.428571 + ch.1.1 2023-02-13 119 4 ch.1.1 0.400000 + + prevalence_rolling + lineage + ba.2 0.677541 + ba.2.10.1 0.095541 + bq.1.1 0.156863 + ch.1.1 0.066667 + +Next we'll collect the prevalence data on each of the four lineages:: + + # Retrieve the official data on the prevalences of these lineages using `daily_prev `_ + d1 = od.daily_prev('ba.2', "IND") + d2 = od.daily_prev('ba.2.10.1', "IND") + d3 = od.daily_prev('bq.1.1', "IND") + d4 = od.daily_prev( 'ch.1.1', "IND") + + # Formatting for creating the graph + d1['lineage'] = 'ba.2' + d2['lineage'] = 'ba.2.10.1' + d3['lineage'] = 'bq.1.1' + d4['lineage'] = 'ch.1.1' + + # Group together data from each lineage + data = pd.concat([d1, d2, d3, d4]) + data = data.rename(columns = {'proportion': 'proportion (%)'}) + + #Pick a date range to analyze + data = data.sort_values(by="date") + data = data.loc[data["date"].between("2022-09-12", "2023-03-31")] + # Increase prevalence by 100% + data['proportion'] = data['proportion'].apply(lambda x: x*100) + + ## Use the visual package of your choice to create an area graph using your data + +.. image:: top4.* diff --git a/_sources/all_lineage_prevalences.rst.txt b/_sources/all_lineage_prevalences.rst.txt new file mode 100644 index 0000000..530c7b4 --- /dev/null +++ b/_sources/all_lineage_prevalences.rst.txt @@ -0,0 +1,42 @@ +all_lineage_prevalences(location, startswith) +--------------------------------------------- + +.. autofunction:: outbreak_data.all_lineage_prevalences + + +Example usage:: + + #Find the prevalence all lineages in Argentina that begin with 'xbb.1' + df = od.prevalence_by_location("ARG", startswith = 'xbb.1') + print(df) + +.. code-block:: + :caption: Output + + date total_count lineage_count lineage prevalence \ + 1454 2022-10-12 3 1 xbb.1 0.333333 + 1455 2022-10-13 0 0 xbb.1 0.000000 + 1456 2022-10-14 0 0 xbb.1 0.000000 + 1457 2022-10-15 0 0 xbb.1 0.000000 + 1458 2022-10-16 0 0 xbb.1 0.000000 + ... ... ... ... ... ... + 1673 2023-03-17 0 0 xbb.1.5 0.000000 + 1674 2023-03-18 0 0 xbb.1.5 0.000000 + 1675 2023-03-19 0 0 xbb.1.5 0.000000 + 1676 2023-03-20 0 0 xbb.1.5 0.000000 + 1677 2023-03-21 1 1 xbb.1.5 1.000000 + + prevalence_rolling + 1454 0.350000 + 1455 0.179487 + 1456 0.109375 + 1457 0.065421 + 1458 0.058577 + ... ... + 1673 1.000000 + 1674 1.000000 + 1675 1.000000 + 1676 1.000000 + 1677 1.000000 + +[224 rows x 6 columns] diff --git a/_sources/auth_setup.rst.txt b/_sources/auth_setup.rst.txt new file mode 100644 index 0000000..32c4602 --- /dev/null +++ b/_sources/auth_setup.rst.txt @@ -0,0 +1,5 @@ +authenticate_new_user() +---------------------------------------------------- + +.. autofunction:: authenticate_user.authenticate_new_user + diff --git a/_sources/cases_by_location.rst.txt b/_sources/cases_by_location.rst.txt new file mode 100644 index 0000000..87d12ef --- /dev/null +++ b/_sources/cases_by_location.rst.txt @@ -0,0 +1,41 @@ +cases_by_location(location) +----------------------------------- + +.. autofunction:: outbreak_data.cases_by_location + +Example usage:: + + #Get the number of SARS-CoV-2 cases in Colorado. + df = outbreak_data.cases_by_location('USA_US-CO') + print(df) + +.. code-block:: + :caption: Output: + + _id _score admin1 confirmed_numIncrease \ + 0 USA_Colorado_None2021-03-14 8.438688 Colorado 505 + 1 USA_Colorado_None2021-03-18 8.438688 Colorado 1060 + 2 USA_Colorado_None2021-03-20 8.438688 Colorado 852 + 3 USA_Colorado_None2021-03-26 8.438688 Colorado 1184 + 4 USA_Colorado_None2021-04-07 8.438688 Colorado 1897 + ... ... ... ... ... + 1116 USA_Colorado_None2022-06-22 8.397695 Colorado 2226 + 1117 USA_Colorado_None2022-06-29 8.397695 Colorado 2402 + 1118 USA_Colorado_None2022-07-09 8.397695 Colorado 1348 + 1119 USA_Colorado_None2022-07-14 8.397695 Colorado 1924 + 1120 USA_Colorado_None2022-07-16 8.397695 Colorado 1231 + + date + 0 2021-03-14 + 1 2021-03-18 + 2 2021-03-20 + 3 2021-03-26 + 4 2021-04-07 + ... ... + 1116 2022-06-22 + 1117 2022-06-29 + 1118 2022-07-09 + 1119 2022-07-14 + 1120 2022-07-16 + +[1121 rows x 5 columns] diff --git a/_sources/collection_date.rst.txt b/_sources/collection_date.rst.txt new file mode 100644 index 0000000..6d2e1e5 --- /dev/null +++ b/_sources/collection_date.rst.txt @@ -0,0 +1,16 @@ +collection_date(pango_lin, mutations=None, location=None) +---------------------------------------------------------- + +.. autofunction:: outbreak_data.collection_date + +Example usage:: + + df = od.collection_date('b.1.1.7', location='IND') + print(df) + +.. code-block:: + :caption: Output + + Values + date 2021-11-26 + date_count 2 diff --git a/_sources/cryptic_vars.rst.txt b/_sources/cryptic_vars.rst.txt new file mode 100644 index 0000000..c07e269 --- /dev/null +++ b/_sources/cryptic_vars.rst.txt @@ -0,0 +1,85 @@ +Tracing Mutations Back to Lineage +--------------------------------- + +The Python Outbreak API can be queried in order to determine which lineages a mutation has been found in. After collecting a sample and determining what sequences are present, we may have a list of several SARS-CoV-2 mutations that we can immediately say are characteristic of a specific variant. However in some cases, we also may have a mutation that is relatively uncommon in most other samples. +For example, we can look at small data sample consisting of 10 mutations: (S:A67V, S:DEL69/70, S:E484A, S:N501Y, S:T572N, S:D614G, S:G142D N:S2Y, S:Q52R, E:L21F, S:G593D). We’ll want a way to find more details about any mutation collected, such as whether the mutation has been collected before, when, and where that mutation came from. + +To start, the ``mutations_by_lineage()`` function allows us to look at the clinical prevalence of a mutation and see which lineage it most likely belongs to. Let's try it for E:L21F:: + + # Perform authentication if you haven't already + from outbreak_data import authenticate_user + authenticate_user.authenticate_new_user() + + # Import outbreak_data package + from outbreak_data import outbreak_data as od + + lin1 = od.mutations_by_lineage(mutation='E:L21F') + print(lin1) + +.. code-block:: + :caption: Output + + pangolin_lineage lineage_count mutation_count proportion \ + 0 ba.2 1228296 560 0.000456 + 1 b.1.1.7 1155169 844 0.000731 + 2 ba.1.1 1046121 268 0.000256 + 3 ay.4 861521 526 0.000611 + 4 ba.1 439838 49 0.000111 + ... ... ... ... ... + 400 ba.2.77 63 48 0.761905 + 401 ba.5.2.54 55 2 0.036364 + 402 b.1.616 39 3 0.076923 + 403 b.1.1.386 20 1 0.050000 + 404 b.1.1.400 20 20 1.000000 + + proportion_ci_lower proportion_ci_upper + 0 0.000419 0.000495 + 1 0.000683 0.000781 + 2 0.000227 0.000288 + 3 0.000560 0.000664 + 4 0.000083 0.000146 + ... ... ... + 400 0.646596 0.853783 + 401 0.007632 0.111568 + 402 0.022142 0.191265 + 403 0.005449 0.210819 + 404 0.883361 0.999976 + +[405 rows x 6 columns] + +This mutation has clearly been seen before in some previous lineages. We might be able recognize that most of the mutations in our list have been detected in older variants, as well as Omicron. However, S:G593D is relatively uncommon in most other samples. We can easily find out where and when it was last detected:: + + >>> lin2 = od.mutations_by_lineage(mutation='S:G593D') + >>> print(lin2) + + pangolin_lineage lineage_count mutation_count proportion \ + 0 xbb.1 28205 1 0.000035 + + proportion_ci_lower proportion_ci_upper + 0 0.000004 0.000166 + + + >>> last_seen = od.collection_date('xbb.1', 'S:G593D') + >>> print(last_seen) + + Values + date 2022-12-12 + date_count 1 + +According to our data, S:G593D has only been detected once in a single sequence belonging to the xbb.1 lineage. The last time it was collected was back on December 12, 2022. + +Additionally ``mutations_by_lineage`` allows us to find out if there is a lineage where several mutations overlap. Selecting 7 of the mutations from our original list yields one lineage with all of these mutation characteristics:: + + >>> lin3 = od.mutations_by_lineage(mutation='S:A67V, S:DEL69/70, S:E484A, S:N501Y, S:T572N, S:D614G, S:G142D') + >>> print(lin3) + + pangolin_lineage lineage_count mutation_count proportion \ + 0 ba.1.19 4587 1 0.000218 + + proportion_ci_lower proportion_ci_upper + 0 0.000024 0.001019 + + +Here we see that the only lineage that contains all 7 mutations is ba.1.19. + + diff --git a/_sources/daily_lag.rst.txt b/_sources/daily_lag.rst.txt new file mode 100644 index 0000000..d6f1d43 --- /dev/null +++ b/_sources/daily_lag.rst.txt @@ -0,0 +1,32 @@ +daily_lag(location=None) +---------------------------- + +.. autofunction:: outbreak_data.daily_lag + +Example usage:: + + df = outbreak_data.daily_lag('LUX') + print(df) + +.. code-block:: + :caption: Output + + Key Values Key Values Key \ + 0 date_collected 2020-02-29 date_collected 2020-02-29 date_collected + 1 date_submitted 2020-03-07 date_submitted 2020-04-02 date_submitted + 2 total_count 1 total_count 1 total_count + + Values Key Values Key Values ... \ + 0 2020-03-05 date_collected 2020-03-06 date_collected 2020-03-07 ... + 1 2020-04-02 date_submitted 2020-04-02 date_submitted 2020-04-02 ... + 2 1 total_count 1 total_count 1 ... + + Key Values Key Values Key \ + 0 date_collected 2023-04-28 date_collected 2023-04-29 date_collected + 1 date_submitted 2023-05-10 date_submitted 2023-05-10 date_submitted + 2 total_count 20 total_count 11 total_count + + Values Key Values Key Values + 0 2023-04-30 date_collected 2023-05-01 date_collected 2023-05-02 + 1 2023-05-10 date_submitted 2023-05-10 date_submitted 2023-05-10 + 2 1 total_count 5 total_count 2 diff --git a/_sources/daily_prev.rst.txt b/_sources/daily_prev.rst.txt new file mode 100644 index 0000000..ed064d2 --- /dev/null +++ b/_sources/daily_prev.rst.txt @@ -0,0 +1,68 @@ +daily_prev(pango_lin, location, mutations, cumulative) +----------------------------------------------------------------------- + +.. autofunction:: outbreak_data.daily_prev + +Example usage: + +1. Get the daily prevalence of lineage 'BA.2' in India since first detection:: + + df1 = od.daily_prev('ba.2', "IND") + print(df1) + +.. code-block:: + :caption: Output + + date total_count lineage_count total_count_rolling \ + 0 2020-08-01 39 1 29.000000 + 1 2020-08-02 100 0 41.285714 + 2 2020-08-03 38 0 42.000000 + 3 2020-08-04 20 0 42.285714 + 4 2020-08-05 26 0 36.000000 + ... ... ... ... ... + 1017 2023-05-15 2 0 5.857143 + 1018 2023-05-16 3 0 5.142857 + 1019 2023-05-17 3 0 3.285714 + 1020 2023-05-18 2 0 3.142857 + 1021 2023-05-20 1 0 2.000000 + + lineage_count_rolling proportion proportion_ci_lower \ + 0 0.142857 0.004926 0.000017 + 1 0.142857 0.003460 0.000012 + 2 0.142857 0.003401 0.000012 + 3 0.142857 0.003378 0.000012 + 4 0.142857 0.003968 0.000014 + ... ... ... ... + 1017 0.000000 0.000000 0.000078 + 1018 0.000000 0.000000 0.000093 + 1019 0.000000 0.000000 0.000151 + 1020 0.000000 0.000000 0.000151 + 1021 0.000000 0.000000 0.000217 + + proportion_ci_upper + 0 0.082286 + 1 0.059076 + 2 0.057719 + 3 0.057719 + 4 0.066944 + ... ... + 1017 0.330389 + 1018 0.379377 + 1019 0.535583 + 1020 0.535583 + 1021 0.666822 + +2. Get a cumulative summary of information regarding 'BA.2' in India:: + + df2 = od.daily_prev('ba.2', "IND", cumulative = True) + print(df2) + +.. code-block:: + :caption: Output + + Values + first_detected 2020-08-01 + global_prevalence 0.109641 + last_detected 2023-04-26 + lineage_count 25561 + total_count 233134 diff --git a/_sources/epidem_analysis.rst.txt b/_sources/epidem_analysis.rst.txt new file mode 100644 index 0000000..82903a5 --- /dev/null +++ b/_sources/epidem_analysis.rst.txt @@ -0,0 +1,86 @@ +Working with epidemiological data +-------------------------------------- +The ``outbreak_data`` package contains endpoints that return epidemiological data on SARS-CoV-2. We can then visualize how SARS-CoV-2 is affecting countries around the world (with the help of one of the many plotting packages available for Python). + +For example, we can look at the pattern of infection counts in California during a specific point in time:: + + # Perform authentication + from outbreak_data import authenticate_user + authenticate_user.authenticate_new_user() + + # Import outbreak_data package + from outbreak_data import outbreak_data as od + import pandas as pd + + # Get the number of increased cases from the previous day in California + counts_ca = od.cases_by_location('USA_US-CA') + # Formatting for graph + counts_ca= counts_ca.rename(columns={"admin1": "location"}) + # Sort info by date and search within a date range + counts_ca = counts_ca.sort_values(by = "date") + counts_ca = counts_ca.loc[counts_ca["date"].between("2021-05-15", "2021-08-15")] + print(counts_ca) + + #Import visual package of choice + import altair as alt + + #Graph! + alt.Chart(xbb_mutations, title = "Daily ORF1a:K47R AND S:T19I Prevalence of Lineage XBB").mark_line().encode( + x='date:T', + y=alt.Y('proportion (%):Q'), + color = 'mutations:N') + + +.. code-block:: + :caption: Output + + _id _score location \ + 621 USA_California_None2021-05-15 8.418888 California + 622 USA_California_None2021-05-16 8.418888 California + 623 USA_California_None2021-05-17 8.418888 California + 624 USA_California_None2021-05-18 8.418888 California + 625 USA_California_None2021-05-19 8.418888 California + .. ... ... ... + 166 USA_California_None2021-08-11 8.419768 California + 644 USA_California_None2021-08-12 8.418888 California + 413 USA_California_None2021-08-13 8.418888 California + 167 USA_California_None2021-08-14 8.419768 California + 414 USA_California_None2021-08-15 8.418888 California + + confirmed_numIncrease date + 621 1504 2021-05-15 + 622 1087 2021-05-16 + 623 793 2021-05-17 + 624 1054 2021-05-18 + 625 1400 2021-05-19 + .. ... ... + 166 11164 2021-08-11 + 644 14356 2021-08-12 + 413 15707 2021-08-13 + 167 13100 2021-08-14 + 414 10744 2021-08-15 + [93 rows x 5 columns] + +.. image:: graphs/ca_cases.png + +We can also do the same analysis over multiple locations and visualize them all at once:: + + counts_ca = od.cases_by_location('USA_US-NY') + counts_ny = od.cases_by_location('USA_US-TX') + counts_fl = od.cases_by_location('USA_US-LA') + counts_wa = od.cases_by_location('USA_US-FL') + + state_count = pd.concat([counts_ca, counts_ny, counts_fl, counts_wa]) + state_count = state_count.rename(columns={"admin1": "location"}) + state_count = state_count.sort_values(by = "date") + state_count = state_count.loc[state_count["date"].between("2020-10-15", "2021-01-15")] + + #Graph it! + alt.Chart(state_count, title = " 90 Day SARS-COV-2 Case Count Increase in Four States").mark_line().encode( + x='date:T', + y=alt.Y('confirmed_numIncrease:Q'), + color = 'location:N') + +.. image:: graphs/multi_state_cases.png + +.. note:: The `Vega-Altair `_ visualization package is used for demonstration purposes. However, any Python visual package can be used to create graphical representations of the data. diff --git a/_sources/genomic_analysis.rst.txt b/_sources/genomic_analysis.rst.txt new file mode 100644 index 0000000..3f727cc --- /dev/null +++ b/_sources/genomic_analysis.rst.txt @@ -0,0 +1,276 @@ +Genomic Analysis +----------------------------------------- + +The ``outbreak_data`` package has contains multiple tools that can collect the relevant genomic information on SARS-CoV-2. Using a combination of these endpoints will allow you to get the information on variants of concern (VoC) and the current mutations to conduct your own multi-level genomic analysis on SARS-CoV-2. On this page, you'll find a few example workflows that demonstrate data manipulation and visualization steps to track the progression of SARS-CoV-2. + +Here is an example workflow that allows the user to manipulate the data to find all the XBB lineages prevalent in India within a 1-year timeframe:: + + # Perform authentication if you haven't already + from outbreak_data import authenticate_user + authenticate_user.authenticate_new_user() + + # Import outbreak_data package + from outbreak_data import outbreak_data as od + + # Get the prevalence of all circulating XBB lineages in India + data = od.prevalence_by_location("IND", startswith = 'xbb') + # multiply prevalence values by 100% for scale + data['prevalence_rolling'] = data['prevalence_rolling'].apply(lambda x: x*100) + # Search for data based on date range + data = data.sort_values(by="date") + data = data.loc[data["date"].between("2020-09-12", "2022-03-31")] + + ## Use the visual package of your choice to create an area graph using your data + import altair as alt + + # Graph of results + alt.Chart(data, title = "Lineage Prevalence in India").mark_area().encode( + x='date:T', + y=alt.Y('prevalence_rolling:Q'), + color = 'lineage:N') + +.. code-block:: + :caption: Output: + + date total_count lineage_count lineage prevalence \ + 3014 2022-09-12 0 0 xbb.1.16 0.000000 + 3781 2022-09-12 0 0 xbb.2.3 0.000000 + 2593 2022-09-12 152 2 xbb.1 0.013158 + 3782 2022-09-13 0 0 xbb.2.3 0.000000 + 3015 2022-09-13 0 0 xbb.1.16 0.000000 + ... ... ... ... ... ... + 4086 2023-03-31 196 2 xbb.2.3.2 0.010204 + 3322 2023-03-31 196 29 xbb.1.16.1 0.147959 + 2793 2023-03-31 196 1 xbb.1 0.005102 + 3381 2023-03-31 196 7 xbb.1.16.2 0.035714 + 3981 2023-03-31 196 15 xbb.2.3 0.076531 + + prevalence_rolling + 3014 0.000000 + 3781 0.000000 + 2593 0.003451 + 3782 0.000000 + 3015 0.000000 + ... ... + 4086 0.031184 + 3322 0.144578 + 2793 0.014174 + 3381 0.045358 + 3981 0.084337 + [985 rows x 6 columns] + +.. image:: graphs/prev_visual.png + +.. note:: The `Vega-Altair `_ visualization package is used for demonstration purposes. However, any Python visual package can be used to create graphical representations of the data. + +**Lineage_Mutations Heatmap** + +A basic but important question: how do we define a lineage? What mutations consistently appear in most sequences within a lineage? We could start by plotting some of the characteristic mutations of XBB occurring in 80% of sequences. Even better, we can do this for mulitple related lineages and compare them using a heatmap:: + + # Collecting 15 characteristic mutations and their prevalences for each variant + lin0 = od.lineage_mutations("xbb", freq = 0.80) + lin0["lineage"] = "xbb" + lin0 = lin0.iloc[:15] + + lin1 = od.lineage_mutations("xbb.1", freq = 0.80) + lin1["lineage"] = "xbb.1" + lin1 = lin1.iloc[:15] + + lin2 = od.lineage_mutations("xbb.1.5", freq = 0.80) + lin2["lineage"] = "xbb.1.5" + lin2 = lin2.iloc[:15] + + lin3 = od.lineage_mutations("xbb.1.16", freq = 0.80) + lin3["lineage"] = "xbb.1.16" + lin3 = lin3.iloc[:15] + + lin4 = od.lineage_mutations("xbb.1.9", freq = 0.80) + lin4["lineage"] = "xbb.1.9" + lin4 = lin4.iloc[:15] + + lin5 = od.lineage_mutations("xbb.2.3", freq = 0.80) + lin5["lineage"] = "xbb.2.3" + lin5 = lin5.iloc[:15] + + # Link each of the findings together for plotting + df = pd.concat([lin0, lin1, lin2, lin3, lin4, lin5]) + df["prevalence"] = df["prevalence"].apply(lambda x: x*100) + df= df.rename(columns={'prevalence': 'prevalence %'}) + + # Plot mutation heatmap + import altair as alt + + alt.Chart(df).mark_rect().encode( + x = "mutation:N", + y = "lineage:N", + color = 'prevalence %:Q') + +.. code-block:: + :caption: Output + + mutation mutation_count lineage_count lineage gene ref_aa alt_aa \ + 0 orf6:d61l 4198 4423 xbb ORF6 D L + 1 s:l24s 3919 4423 xbb S L S + 2 n:r203k 4378 4423 xbb N R K + 3 s:g339h 4054 4423 xbb S G H + 4 s:v445p 3643 4423 xbb S V P + ... ... ... ... ... ... ... ... + 10 orf1a:p3395h 3263 3279 xbb.2.3 ORF1a P H + 11 s:n969k 3261 3279 xbb.2.3 S N K + 12 orf1a:g1307s 3257 3279 xbb.2.3 ORF1a G S + 13 s:d614g 3257 3279 xbb.2.3 S D G + 14 s:q954h 3257 3279 xbb.2.3 S Q H + + codon_num codon_end type prevalence % change_length_nt + 0 61 None substitution 94.912955 None + 1 24 None substitution 88.605019 None + 2 203 None substitution 98.982591 None + 3 339 None substitution 91.657246 None + 4 445 None substitution 82.364911 None + ... ... ... ... ... ... + 10 3395 None substitution 99.512046 None + 11 969 None substitution 99.451052 None + 12 1307 None substitution 99.329064 None + 13 614 None substitution 99.329064 None + 14 954 None substitution 99.329064 None + +[90 rows x 12 columns] + + +.. image:: graphs/mut_by_lin.png + +**Comparing Lineages** + +To better understand the evolution of SARS-CoV-2, we may also want to know what mutations are shared between different viral lineages and how many shared mutations there are. + +For this example we'll look at three different lineages: B.1.1.7, P.1, and B.1.1.529. First, let's get an idea of which mutations are shared between all three lineages:: + + lin1 = od.lineage_mutations("b.1.1.7") + lin1["lineage"] = "b.1.1.7" + + lin2 = od.lineage_mutations("P.1") + lin2["lineage"] = "P.1" + + lin3 = od.lineage_mutations("b.1.1.529") + lin3["lineage"] = "b.1.1.529" + + #Finding intersections + + #Created an optional but convenient intersecting function + def intersect(lst1, lst2): + return set(lst1).intersection(lst2) + + a = set(lin1['mutation']) + b = set(lin2['mutation']) + c = set(lin3['mutation']) + + m12 = intersect(a, b) + m13 = intersect(a, c) + m23 = intersect(b, c) + m123 = intersect(m12, c) + + print('Set 1.2:', m12) + print('Set 1.3:', m13) + print('Set 2.3:' , m23) + print('Set 1.2.3:', m123) + +.. code-block:: + :caption: Output + + Set 1.2: {'orf1b:p314l', 'orf8:s84l', 'orf1a:del3675/3677', 'n:r203k', 's:d614g', 's:n501y', 'n:g204r'} + Set 1.3: {'s:p681h', 'orf1b:p314l', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'} + Set 2.3: {'orf1b:p314l', 's:h655y', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'} + Set 1.2.3: {'orf1b:p314l', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'} + + +Finally, we can make a visual based on our findings and create a Venn diagram of our results:: + + # Import libraries for venn diagram visual + from matplotlib_venn import venn3, venn3_circles + from matplotlib import pyplot as plt + + # Using matplotlib_venn to make venn diagram with custom visuals + ## The venn diagram package used here automatically determines the number + ## of intersecting values and plots accordingly + + vd3 = venn3([a, b, c], set_labels = ('Alpha/B.1.1.7', 'Gamma/P.1', 'Omicron/B.1.1.529'), set_colors=('#c4e6ff', '#F4ACB7','#9D8189'), + alpha = 0.8) + c = venn3_circles([a, b, c,], linestyle = '-.', linewidth=2, color='grey') + for text in vd3.set_labels: + text.set_fontsize(16); + for text in vd3.subset_labels: + text.set_fontsize(16) + plt.title('Number of Overlapping Mutations in 3 Variants',fontname ='Helvetica',fontweight ='bold',fontsize = 18, + pad = 30,backgroundcolor ='#cbe7e3',color ='black', style ='normal'); + c[0].set_lw(7.0) + c[0].set_ls(':') + plt.show() + +.. image:: graphs/compare.png + +We can see that the graph matches the number of intersecting mutations that we previously saw, given that the venn diagram also takes into account unique values for each set. + +.. note:: Please see the `matplotlib venn diagram documentation `_ and `this article `_ for more info on how to create these graphs. + +**Finding the Most Prevalent Lineages** + +If we wanted to determine and plot the top four most prevalent lineages in India, we can make a few queries and use a few simple commands to create a table that shows us what these lineages are:: + + data=od.prevalence_by_location("IND") + most_prev = data.groupby('lineage').apply(max) # Finds the lineages with the most hits + most_prev = most_prev.mask(most_prev == '').dropna(how = 'any') # Drop any unknowns + most_prev = most_prev.iloc[:4] + print(most_prev) + +.. code-block:: + :caption: Output + + date total_count lineage_count lineage prevalence \ + lineage + ba.2 2023-04-20 5668 1445 ba.2 0.822785 + ba.2.10.1 2023-04-19 5668 93 ba.2.10.1 0.285714 + bq.1.1 2023-03-27 402 7 bq.1.1 0.428571 + ch.1.1 2023-02-13 119 4 ch.1.1 0.400000 + + prevalence_rolling + lineage + ba.2 0.677541 + ba.2.10.1 0.095541 + bq.1.1 0.156863 + ch.1.1 0.066667 + +Next we'll collect the prevalence data on each of the four lineages:: + + # Retrieve the official data on the prevalences of these lineages using `daily_prev()` + d1 = od.daily_prev('ba.2', "IND") + d2 = od.daily_prev('ba.2.10.1', "IND") + d3 = od.daily_prev('bq.1.1', "IND") + d4 = od.daily_prev( 'ch.1.1', "IND") + + # Formatting for creating the graph + d1['lineage'] = 'ba.2' + d2['lineage'] = 'ba.2.10.1' + d3['lineage'] = 'bq.1.1' + d4['lineage'] = 'ch.1.1' + + # Group together data from each lineage + data = pd.concat([d1, d2, d3, d4]) + data = data.rename(columns = {'proportion': 'proportion (%)'}) + + #Pick a date range to analyze + data = data.sort_values(by="date") + data = data.loc[data["date"].between("2022-09-12", "2023-03-31")] + # Increase prevalence by 100% + data['proportion'] = data['proportion'].apply(lambda x: x*100) + + #Graph using preferred visual package + import altair as alt + alt.Chart(data, title = "Top 4 Most Prevalent Lineages in India").mark_area().encode( + x='date:T', + y=alt.Y('proportion (%):Q'), + color = 'lineage:N') + + +.. image:: graphs/top4.png + + diff --git a/_sources/global_prevalence.rst.txt b/_sources/global_prevalence.rst.txt new file mode 100644 index 0000000..02fa271 --- /dev/null +++ b/_sources/global_prevalence.rst.txt @@ -0,0 +1,55 @@ +global_prevalence(pango_lin, mutations, cumulative, lineage_crumbs=False) +-------------------------------------------------------------------------- + +.. autofunction:: outbreak_data.global_prevalence + +Example: Get global info on lineage 'XBB':: + + df = outbreak_data.global_prevalence('xbb') + print(df) + +.. code-block:: + :caption: Output: + + date total_count lineage_count total_count_rolling \ + 0 2021-06-29 15453 2 10772.428571 + 1 2021-06-30 13101 0 11060.571429 + 2 2021-07-01 13088 0 11495.000000 + 3 2021-07-02 11562 0 11890.571429 + 4 2021-07-03 8310 0 11845.571429 + .. ... ... ... ... + 713 2023-06-12 27 0 112.428571 + 714 2023-06-13 8 0 61.714286 + 715 2023-06-14 1 0 36.000000 + 716 2023-06-15 1 0 25.285714 + 717 2023-06-17 1 0 8.000000 + + lineage_count_rolling proportion proportion_ci_lower \ + 0 0.285714 0.000027 4.558329e-08 + 1 0.285714 0.000026 4.439232e-08 + 2 0.285714 0.000025 4.271630e-08 + 3 0.285714 0.000024 4.129377e-08 + 4 0.285714 0.000024 4.145063e-08 + .. ... ... ... + 713 0.142857 0.001271 4.374452e-06 + 714 0.000000 0.000000 7.888011e-06 + 715 0.000000 0.000000 1.354537e-05 + 716 0.000000 0.000000 1.944577e-05 + 717 0.000000 0.000000 5.949030e-05 + + proportion_ci_upper + 0 0.000233 + 1 0.000227 + 2 0.000218 + 3 0.000211 + 4 0.000212 + .. ... + 713 0.022129 + 714 0.039548 + 715 0.066944 + 716 0.094683 + 717 0.262217 + +[718 rows x 8 columns] + + diff --git a/_sources/growth_rates.rst.txt b/_sources/growth_rates.rst.txt new file mode 100644 index 0000000..152366e --- /dev/null +++ b/_sources/growth_rates.rst.txt @@ -0,0 +1,4 @@ +growth_rates(lineage, location) +------------------------------- + +.. autofunction:: outbreak_data.growth_rates diff --git a/_sources/id_lookup.rst.txt b/_sources/id_lookup.rst.txt new file mode 100644 index 0000000..50ff352 --- /dev/null +++ b/_sources/id_lookup.rst.txt @@ -0,0 +1,5 @@ +id_lookup(locations, max_results = 10, table = False) +---------------------------------------------------------- + +.. autofunction:: outbreak_tools + diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt new file mode 100644 index 0000000..1b1177f --- /dev/null +++ b/_sources/index.rst.txt @@ -0,0 +1,83 @@ +.. Py_Outbreak_API documentation master file, created by + sphinx-quickstart on Sat Oct 8 22:16:44 2022. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to the Python Outbreak.info package docs! +======================================================== +Here you can find information on the functions you will use to collect and analyze SARS-COV-2 data from the Outbreak.info API. +Our package pulls data from the `Outbreak.info API `_ and is reflected on our `Outbreak.info web interface `_ + +Installation +---------------- +We recommend installing the package via pip using: + +``pip install python-outbreak-info`` + +Alternatively, the package can be directly installed from source via pip: + +``pip install git+https://github.com/outbreak-info/python-outbreak-info.git`` + +Getting Started +---------------- +The Python Outbreak.info package contains key functions for accessing genomic and epidemiological data for SARS-CoV-2. Access to genomic data requires logging in using GISAID credentials to generate an API key, using the ``authenticate_new_user()`` function. To perform authentication, you'll need to first run + +.. code-block:: python + + from outbreak_data import authenticate_user + authenticate_user.authenticate_new_user() + +and then you should be able access all of the functionality of the package. Most of the rest of the tools are available within the ``outbreak_data`` component of the package. For example: + +.. code-block:: python + + from outbreak_data import outbreak_data + lin_list = ['B.1.1.7','B.1.351','B.1.617.2'] + # request lineages occurring with minimum frequency of 0.05 (5%) + df = outbreak_data.lineage_mutations(lin_list,freq=0.05) + # filter mutations and sort by codon number + df = df[df['gene']=='S'].sort_values(by='codon_num') + +For location-specific analyses, users will need to supply the appropriate location code corresponding to their location of interest. To do this, we provide an ID lookup tool kit via the ``outbreak_tools`` part of the package. An example lookup should look like: + +.. code-block:: python + + from outbreak_tools import outbreak_tools + location_list = outbreak_tools.id_lookup(['Illinois','South Africa','Chile']) + # which returns ['USA_US-IL', 'ZAF', 'CHL'] + + +.. note:: + + This project is under active development. + +Core Outbreak Data Tools +-------------------------- +.. toctree:: + auth_setup + cases_by_location + lineage_mutations + all_lineage_prevalences + global_prevalence + seq_counts + mutations_by_lineage + prevalence_by_location + lineage_by_sub_admin + collection_date + submission_date + mutation_details + daily_lag + wildcard_lineage + wildcard_location + wildcard_mutations + location_details + outbreak_data_functions + growth_rates + +Example analyses: +-------------------------- +.. toctree:: + Epidemiological data analyses + Lineage Prevalence Analyses + Mutation Data Analyses + Dealing with Cryptic Variants diff --git a/_sources/lineage_by_sub_admin.rst.txt b/_sources/lineage_by_sub_admin.rst.txt new file mode 100644 index 0000000..0cb5f4b --- /dev/null +++ b/_sources/lineage_by_sub_admin.rst.txt @@ -0,0 +1,39 @@ +lineage_by_sub_admin(pango_lin, mutations, location, ndays=0, detected) +----------------------------------------------------------------------- + +.. autofunction:: outbreak_data.lineage_by_sub_admin + +Example usage:: + + df = od.lineage_by_sub_admin('xbb.1.15', location='FRA') + print(df) + +.. code-block:: + :caption: Output: + + date name id total_count lineage_count \ + 0 2023-06-04 FRA_FR-none 3 0 + 1 2023-05-31 Bretagne FRA_FR-BT 2 0 + 2 2023-05-22 Corse FRA_FR-CE 1 0 + 3 2023-05-30 Grand Est FRA_FR-AO 68 0 + 4 2023-06-04 Normandie FRA_FR-ND 2 0 + 5 2023-06-01 Occitanie FRA_FR-LP 2 0 + 6 2023-05-30 Pays de la Loire FRA_FR-PL 22 0 + + cum_total_count cum_lineage_count proportion proportion_ci_lower \ + 0 406320 10 0.000025 1.265376e-05 + 1 22070 1 0.000045 4.888926e-06 + 2 2007 0 0.000000 2.446305e-07 + 3 43954 1 0.000023 2.454796e-06 + 4 19479 0 0.000000 2.520808e-08 + 5 57933 0 0.000000 8.475868e-09 + 6 24556 0 0.000000 1.999632e-08 + + proportion_ci_upper + 0 0.000044 + 1 0.000212 + 2 0.001251 + 3 0.000106 + 4 0.000129 + 5 0.000043 + 6 0.000102 diff --git a/_sources/lineage_mutations.rst.txt b/_sources/lineage_mutations.rst.txt new file mode 100644 index 0000000..b8a62de --- /dev/null +++ b/_sources/lineage_mutations.rst.txt @@ -0,0 +1,163 @@ +lineage_mutations(pango_lin, mutation, freq) +-------------------------------------------- + +.. autofunction:: outbreak_data.lineage_mutations + +Example usage: + +1. Get a list of all mutations and relevant data associated with the variant 'B.1.1.7':: + + df = outbreak_data.lineage_mutations('b.1.1.7') + print(df) + +.. code-block:: + :caption: Output: + + mutation mutation_count lineage_count lineage gene \ + 0 n:d3l 1133368 1154337 b.1.1.7 N + 1 n:r203k 1131899 1154337 b.1.1.7 N + 2 s:d614g 1150796 1154337 b.1.1.7 S + 3 orf1a:t1001i 1149579 1154337 b.1.1.7 ORF1a + 4 orf8:s84l 1148665 1154337 b.1.1.7 ORF8 + 5 s:a570d 1147678 1154337 b.1.1.7 S + 6 s:p681h 1147591 1154337 b.1.1.7 S + 7 orf1b:p314l 1147331 1154337 b.1.1.7 ORF1b + 8 s:d1118h 1147009 1154337 b.1.1.7 S + 9 orf1a:a1708d 1146288 1154337 b.1.1.7 ORF1a + 10 orf8:y73c 1144041 1154337 b.1.1.7 ORF8 + 11 s:s982a 1142512 1154337 b.1.1.7 S + 12 orf8:q27* 1142465 1154337 b.1.1.7 ORF8 + 13 s:t716i 1142087 1154337 b.1.1.7 S + 14 n:s235f 1141424 1154337 b.1.1.7 N + 15 orf8:r52i 1138388 1154337 b.1.1.7 ORF8 + 16 s:n501y 1129018 1154337 b.1.1.7 S + 17 orf1a:i2230t 1127643 1154337 b.1.1.7 ORF1a + 18 orf1a:del3675/3677 1115708 1154337 b.1.1.7 ORF1a + 19 s:del69/70 1114288 1154337 b.1.1.7 S + 20 s:del144/144 1093432 1154337 b.1.1.7 S + 21 n:g204r 1050444 1154337 b.1.1.7 N + + ref_aa alt_aa codon_num codon_end type \ + 0 D L 3 None substitution + 1 R K 203 None substitution + 2 D G 614 None substitution + 3 T I 1001 None substitution + 4 S L 84 None substitution + 5 A D 570 None substitution + 6 P H 681 None substitution + 7 P L 314 None substitution + 8 D H 1118 None substitution + 9 A D 1708 None substitution + 10 Y C 73 None substitution + 11 S A 982 None substitution + 12 Q * 27 None substitution + 13 T I 716 None substitution + 14 S F 235 None substitution + 15 R I 52 None substitution + 16 N Y 501 None substitution + 17 I T 2230 None substitution + 18 ORF1A:DEL3675/3677 DEL3675/3677 3675 3677.0 deletion + 19 S:DEL69/70 DEL69/70 69 70.0 deletion + 20 S:DEL144/144 DEL144/144 144 144.0 deletion + 21 G R 204 None substitution + + prevalence change_length_nt + 0 0.981835 None + 1 0.980562 None + 2 0.996932 None + 3 0.995878 None + 4 0.995086 None + 5 0.994231 None + 6 0.994156 None + 7 0.993931 None + 8 0.993652 None + 9 0.993027 None + 10 0.991081 None + 11 0.989756 None + 12 0.989715 None + 13 0.989388 None + 14 0.988813 None + 15 0.986183 None + 16 0.978066 None + 17 0.976875 None + 18 0.966536 9.0 + 19 0.965306 6.0 + 20 0.947238 3.0 + 21 0.909998 None + +2. Mutiple queries for lineages and mutations can be separated by ",":: + + #Find mutation information for B.1.1.7, P.1, and XBB.1.5 + df = outbreak_data_lineage_mutations('b.1.1.7, p.1, xbb.1.5') + print(df) + +.. code-block:: + :caption: Output + + mutation mutation_count lineage_count lineage gene ref_aa \ + 0 n:d3l 1133368 1154337 b.1.1.7 N D + 1 n:r203k 1131899 1154337 b.1.1.7 N R + 2 s:d614g 1150796 1154337 b.1.1.7 S D + 3 orf1a:t1001i 1149579 1154337 b.1.1.7 ORF1a T + 4 orf8:s84l 1148665 1154337 b.1.1.7 ORF8 S + .. ... ... ... ... ... ... + 63 s:g446s 156244 167128 xbb.1.5 S G + 64 s:del144/144 154766 167128 xbb.1.5 S S:DEL144/144 + 65 s:h146q 153308 167128 xbb.1.5 S H + 66 s:r408s 152365 167128 xbb.1.5 S R + 67 s:k417n 147604 167128 xbb.1.5 S K + + alt_aa codon_num codon_end type prevalence change_length_nt + 0 L 3 None substitution 0.981835 None + 1 K 203 None substitution 0.980562 None + 2 G 614 None substitution 0.996932 None + 3 I 1001 None substitution 0.995878 None + 4 L 84 None substitution 0.995086 None + .. ... ... ... ... ... ... + 63 S 446 None substitution 0.934876 None + 64 DEL144/144 144 144.0 deletion 0.926033 3.0 + 65 Q 146 None substitution 0.917309 None + 66 S 408 None substitution 0.911667 None + 67 N 417 None substitution 0.883179 None + +[113 rows x 12 columns] + +3. Use 'OR' in a string to return overlapping mutations in multiple lineages:: + + df = outbreak_data.lineage_mutations('ba.2 OR xbb.1.5') + print(df) + +.. code-block:: + :caption: Output + + mutation mutation_count lineage_count lineage gene \ + 0 n:r203k 237984 243206 P.1 OR xbb.1.5 N + 1 s:d614g 242522 243206 P.1 OR xbb.1.5 S + 2 orf1b:p314l 242226 243206 P.1 OR xbb.1.5 ORF1b + 3 s:h655y 241765 243206 P.1 OR xbb.1.5 S + 4 orf8:s84l 240116 243206 P.1 OR xbb.1.5 ORF8 + 5 n:g204r 238101 243206 P.1 OR xbb.1.5 N + 6 s:n501y 235654 243206 P.1 OR xbb.1.5 S + 7 orf1a:del3675/3677 226006 243206 P.1 OR xbb.1.5 ORF1a + + ref_aa alt_aa codon_num codon_end type \ + 0 R K 203 None substitution + 1 D G 614 None substitution + 2 P L 314 None substitution + 3 H Y 655 None substitution + 4 S L 84 None substitution + 5 G R 204 None substitution + 6 N Y 501 None substitution + 7 ORF1A:DEL3675/3677 DEL3675/3677 3675 3677.0 deletion + + prevalence change_length_nt + 0 0.978528 None + 1 0.997188 None + 2 0.995970 None + 3 0.994075 None + 4 0.987295 None + 5 0.979010 None + 6 0.968948 None + 7 0.929278 9.0 + + diff --git a/_sources/lineage_prevalence.rst.txt b/_sources/lineage_prevalence.rst.txt new file mode 100644 index 0000000..38bf843 --- /dev/null +++ b/_sources/lineage_prevalence.rst.txt @@ -0,0 +1,127 @@ +Lineage Prevalence Analysis +----------------------------------------- + +The ``outbreak_data`` package has contains multiple endpoints that can collect information on SARS-CoV-2 lineages. Pulling data from a combination of endpoints will allow you to conduct your own analysis on the progression of SARS-CoV-2. On this page, you'll find a few example workflows that demonstrate how to collect, manipulate, and visualize prevalence data in SARS-CoV-2 lineages. + +Here is how we would go about collecting data to find all the XBB lineages prevalent in India within a 1-year timeframe:: + + # Perform authentication if you haven't already + from outbreak_data import authenticate_user + authenticate_user.authenticate_new_user() + + # Import outbreak_data package + from outbreak_data import outbreak_data as od + + # Get the prevalence of all circulating XBB lineages in India + data = od.prevalence_by_location("IND", startswith = 'xbb') + # multiply prevalence values by 100% for scale + data['prevalence_rolling'] = data['prevalence_rolling'].apply(lambda x: x*100) + # Search for data based on date range + data = data.sort_values(by="date") + data = data.loc[data["date"].between("2020-09-12", "2022-03-31")] + + ## Use the visual package of your choice to create an area graph using your data + import altair as alt + + # Graph of results + alt.Chart(data, title = "Lineage Prevalence in India").mark_area().encode( + x='date:T', + y=alt.Y('prevalence_rolling:Q'), + color = 'lineage:N') + +.. code-block:: + :caption: Output: + + date total_count lineage_count lineage prevalence \ + 3014 2022-09-12 0 0 xbb.1.16 0.000000 + 3781 2022-09-12 0 0 xbb.2.3 0.000000 + 2593 2022-09-12 152 2 xbb.1 0.013158 + 3782 2022-09-13 0 0 xbb.2.3 0.000000 + 3015 2022-09-13 0 0 xbb.1.16 0.000000 + ... ... ... ... ... ... + 4086 2023-03-31 196 2 xbb.2.3.2 0.010204 + 3322 2023-03-31 196 29 xbb.1.16.1 0.147959 + 2793 2023-03-31 196 1 xbb.1 0.005102 + 3381 2023-03-31 196 7 xbb.1.16.2 0.035714 + 3981 2023-03-31 196 15 xbb.2.3 0.076531 + + prevalence_rolling + 3014 0.000000 + 3781 0.000000 + 2593 0.003451 + 3782 0.000000 + 3015 0.000000 + ... ... + 4086 0.031184 + 3322 0.144578 + 2793 0.014174 + 3381 0.045358 + 3981 0.084337 + [985 rows x 6 columns] + +.. image:: graphs/prev_visual.png + +.. note:: The `Vega-Altair `_ visualization package is used for demonstration purposes. However, any Python visual package can be used to create graphical representations of the data. + +**Finding the Most Prevalent Lineages** + +If we wanted to determine and plot the top four most prevalent lineages in India, we can make a few queries and use a few simple commands to create a table that shows us what these lineages are:: + + data=od.prevalence_by_location("IND") + most_prev = data.groupby('lineage').apply(max) # Finds the lineages with the most hits + most_prev = most_prev.mask(most_prev == '').dropna(how = 'any') # Drop any unknowns + most_prev = most_prev.iloc[:4] + print(most_prev) + +.. code-block:: + :caption: Output + + date total_count lineage_count lineage prevalence \ + lineage + ba.2 2023-04-20 5668 1445 ba.2 0.822785 + ba.2.10.1 2023-04-19 5668 93 ba.2.10.1 0.285714 + bq.1.1 2023-03-27 402 7 bq.1.1 0.428571 + ch.1.1 2023-02-13 119 4 ch.1.1 0.400000 + + prevalence_rolling + lineage + ba.2 0.677541 + ba.2.10.1 0.095541 + bq.1.1 0.156863 + ch.1.1 0.066667 + +Next we'll collect the prevalence data on each of the four lineages:: + + # Retrieve the official data on the prevalences of these lineages using `daily_prev()` + d1 = od.daily_prev('ba.2', "IND") + d2 = od.daily_prev('ba.2.10.1', "IND") + d3 = od.daily_prev('bq.1.1', "IND") + d4 = od.daily_prev( 'ch.1.1', "IND") + + # Formatting for creating the graph + d1['lineage'] = 'ba.2' + d2['lineage'] = 'ba.2.10.1' + d3['lineage'] = 'bq.1.1' + d4['lineage'] = 'ch.1.1' + + # Group together data from each lineage + data = pd.concat([d1, d2, d3, d4]) + data = data.rename(columns = {'proportion': 'proportion (%)'}) + + #Pick a date range to analyze + data = data.sort_values(by="date") + data = data.loc[data["date"].between("2022-09-12", "2023-03-31")] + # Increase prevalence by 100% + data['proportion'] = data['proportion'].apply(lambda x: x*100) + + #Graph using preferred visual package + import altair as alt + alt.Chart(data, title = "Top 4 Most Prevalent Lineages in India").mark_area().encode( + x='date:T', + y=alt.Y('proportion (%):Q'), + color = 'lineage:N') + + +.. image:: graphs/top4.png + + diff --git a/_sources/location_details.rst.txt b/_sources/location_details.rst.txt new file mode 100644 index 0000000..ac04fe4 --- /dev/null +++ b/_sources/location_details.rst.txt @@ -0,0 +1,5 @@ +location_details(location) +--------------------------- + +.. autofunction:: outbreak_data.location_details + diff --git a/_sources/mutation_analysis.rst.txt b/_sources/mutation_analysis.rst.txt new file mode 100644 index 0000000..7c261ed --- /dev/null +++ b/_sources/mutation_analysis.rst.txt @@ -0,0 +1,161 @@ +Viral Mutation Analysis +------------------------- + +**Lineage_Mutations Heatmap** + +A basic but important question: how do we define a lineage? What mutations consistently appear in most sequences within a lineage? We could start by plotting some of the characteristic mutations of XBB occurring in 80% of sequences. Even better, we can do this for mulitple related lineages and compare them using a heatmap:: + + # Perform authentication if you haven't already + from outbreak_data import authenticate_user + authenticate_user.authenticate_new_user() + + # Import outbreak_data package + from outbreak_data import outbreak_data as od + + + # Collecting 15 characteristic mutations and their prevalences for each variant + + lin0 = od.lineage_mutations("xbb", freq = 0.80) + lin0["lineage"] = "xbb" + lin0 = lin0.iloc[:15] + + lin1 = od.lineage_mutations("xbb.1", freq = 0.80) + lin1["lineage"] = "xbb.1" + lin1 = lin1.iloc[:15] + + lin2 = od.lineage_mutations("xbb.1.5", freq = 0.80) + lin2["lineage"] = "xbb.1.5" + lin2 = lin2.iloc[:15] + + lin3 = od.lineage_mutations("xbb.1.16", freq = 0.80) + lin3["lineage"] = "xbb.1.16" + lin3 = lin3.iloc[:15] + + lin4 = od.lineage_mutations("xbb.1.9", freq = 0.80) + lin4["lineage"] = "xbb.1.9" + lin4 = lin4.iloc[:15] + + lin5 = od.lineage_mutations("xbb.2.3", freq = 0.80) + lin5["lineage"] = "xbb.2.3" + lin5 = lin5.iloc[:15] + + # Link each of the findings together for plotting + df = pd.concat([lin0, lin1, lin2, lin3, lin4, lin5]) + df["prevalence"] = df["prevalence"].apply(lambda x: x*100) + df= df.rename(columns={'prevalence': 'prevalence %'}) + + # Plot mutation heatmap + import altair as alt + + alt.Chart(df).mark_rect().encode( + x = "mutation:N", + y = "lineage:N", + color = 'prevalence %:Q') + +.. code-block:: + :caption: Output + + mutation mutation_count lineage_count lineage gene ref_aa alt_aa \ + 0 orf6:d61l 4198 4423 xbb ORF6 D L + 1 s:l24s 3919 4423 xbb S L S + 2 n:r203k 4378 4423 xbb N R K + 3 s:g339h 4054 4423 xbb S G H + 4 s:v445p 3643 4423 xbb S V P + ... ... ... ... ... ... ... ... + 10 orf1a:p3395h 3263 3279 xbb.2.3 ORF1a P H + 11 s:n969k 3261 3279 xbb.2.3 S N K + 12 orf1a:g1307s 3257 3279 xbb.2.3 ORF1a G S + 13 s:d614g 3257 3279 xbb.2.3 S D G + 14 s:q954h 3257 3279 xbb.2.3 S Q H + + codon_num codon_end type prevalence % change_length_nt + 0 61 None substitution 94.912955 None + 1 24 None substitution 88.605019 None + 2 203 None substitution 98.982591 None + 3 339 None substitution 91.657246 None + 4 445 None substitution 82.364911 None + ... ... ... ... ... ... + 10 3395 None substitution 99.512046 None + 11 969 None substitution 99.451052 None + 12 1307 None substitution 99.329064 None + 13 614 None substitution 99.329064 None + 14 954 None substitution 99.329064 None + +[90 rows x 12 columns] + + +.. image:: graphs/mut_by_lin.png + +**Comparing Lineages** + +To better understand the evolution of SARS-CoV-2, we may also want to know what mutations are shared between different viral lineages and how many shared mutations there are. + +For this example we'll look at three different lineages: B.1.1.7, P.1, and B.1.1.529. First, let's get an idea of which mutations are shared between all three lineages:: + + lin1 = od.lineage_mutations("b.1.1.7") + lin1["lineage"] = "b.1.1.7" + + lin2 = od.lineage_mutations("P.1") + lin2["lineage"] = "P.1" + + lin3 = od.lineage_mutations("b.1.1.529") + lin3["lineage"] = "b.1.1.529" + + #Finding intersections + + #Created an optional but convenient intersecting function + def intersect(lst1, lst2): + return set(lst1).intersection(lst2) + + a = set(lin1['mutation']) + b = set(lin2['mutation']) + c = set(lin3['mutation']) + + m12 = intersect(a, b) + m13 = intersect(a, c) + m23 = intersect(b, c) + m123 = intersect(m12, c) + + print('Set 1.2:', m12) + print('Set 1.3:', m13) + print('Set 2.3:' , m23) + print('Set 1.2.3:', m123) + +.. code-block:: + :caption: Output + + Set 1.2: {'orf1b:p314l', 'orf8:s84l', 'orf1a:del3675/3677', 'n:r203k', 's:d614g', 's:n501y', 'n:g204r'} + Set 1.3: {'s:p681h', 'orf1b:p314l', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'} + Set 2.3: {'orf1b:p314l', 's:h655y', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'} + Set 1.2.3: {'orf1b:p314l', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'} + + +Finally, we can make a visual based on our findings and create a Venn diagram of our results:: + + # Import libraries for venn diagram visual + from matplotlib_venn import venn3, venn3_circles + from matplotlib import pyplot as plt + + # Using matplotlib_venn to make venn diagram with custom visuals + ## The venn diagram package used here automatically determines the number + ## of intersecting values and plots accordingly + + vd3 = venn3([a, b, c], set_labels = ('Alpha/B.1.1.7', 'Gamma/P.1', 'Omicron/B.1.1.529'), set_colors=('#c4e6ff', '#F4ACB7','#9D8189'), + alpha = 0.8) + c = venn3_circles([a, b, c,], linestyle = '-.', linewidth=2, color='grey') + for text in vd3.set_labels: + text.set_fontsize(16); + for text in vd3.subset_labels: + text.set_fontsize(16) + plt.title('Number of Overlapping Mutations in 3 Variants',fontname ='Helvetica',fontweight ='bold',fontsize = 18, + pad = 30,backgroundcolor ='#cbe7e3',color ='black', style ='normal'); + c[0].set_lw(7.0) + c[0].set_ls(':') + plt.show() + +.. image:: graphs/compare.png + +We can see that the graph matches the number of intersecting mutations that we previously saw, given that the venn diagram also takes into account unique values for each set. + +.. note:: Please see the `matplotlib venn diagram documentation `_ and `this article `_ for more info on how to create these graphs. + diff --git a/_sources/mutation_details.rst.txt b/_sources/mutation_details.rst.txt new file mode 100644 index 0000000..1e512a8 --- /dev/null +++ b/_sources/mutation_details.rst.txt @@ -0,0 +1,27 @@ +mutation_details(mutations) +---------------------------- + +.. autofunction:: outbreak_data.mutation_details + +Example usage:: + + #Get info on mutation 'orf1b:p314l' + df = outbreak_data.mutation_details('orf1b:p314l') + print(df) + +.. code-block:: + :caption: Output + + Key Values + 0 mutation ORF1b:P314L + 1 alt_codon CTT + 2 is_synonymous False + 3 codon_num 314 + 4 ref_codon CCT + 5 gene ORF1b + 6 pos 14407 + 7 alt_aa L + 8 ref_aa P + 9 type substitution + + diff --git a/_sources/mutations_by_lineage.rst.txt b/_sources/mutations_by_lineage.rst.txt new file mode 100644 index 0000000..704e94d --- /dev/null +++ b/_sources/mutations_by_lineage.rst.txt @@ -0,0 +1,44 @@ +mutations_by_lineage(mutation, location, pango_lin) +--------------------------------------------------- + +.. autofunction:: outbreak_data.mutations_by_lineage + + +Example usage:: + + #Get info on mutation 'orf1b:p314l' + df = od.mutations_by_lineage('orf1b:p314l') + print(df) + +.. code-block:: + :caption: Output + + pangolin_lineage lineage_count mutation_count proportion \ + 0 ba.2 1227503 1222717 0.996101 + 1 b.1.1.7 1154337 1147331 0.993931 + 2 ba.1.1 1044480 1039813 0.995532 + 3 ay.4 858839 854935 0.995454 + 4 ba.1 438947 437207 0.996036 + ... ... ... ... ... + 2851 fn.1 1 1 1.000000 + 2852 miscba1ba2post5386 1 1 1.000000 + 2853 xbb.1.23 1 1 1.000000 + 2854 xbb.1.37 1 1 1.000000 + 2855 xbv 1 1 1.000000 + + proportion_ci_lower proportion_ci_upper + 0 0.995990 0.996210 + 1 0.993788 0.994071 + 2 0.995402 0.995658 + 3 0.995310 0.995595 + 4 0.995847 0.996219 + ... ... ... + 2851 0.146746 0.999614 + 2852 0.146746 0.999614 + 2853 0.146746 0.999614 + 2854 0.146746 0.999614 + 2855 0.146746 0.999614 + +[2856 rows x 6 columns] + + diff --git a/_sources/outbreak_data_Functions.rst.txt b/_sources/outbreak_data_Functions.rst.txt new file mode 100644 index 0000000..fe550d8 --- /dev/null +++ b/_sources/outbreak_data_Functions.rst.txt @@ -0,0 +1,15 @@ +get_outbreak_data() +--------------------------------- +.. note:: + + This is a hidden function. + + +.. autofunction:: outbreak_data.get_outbreak_data + + + + + + + diff --git a/_sources/outbreak_data_functions.rst.txt b/_sources/outbreak_data_functions.rst.txt new file mode 100644 index 0000000..fe550d8 --- /dev/null +++ b/_sources/outbreak_data_functions.rst.txt @@ -0,0 +1,15 @@ +get_outbreak_data() +--------------------------------- +.. note:: + + This is a hidden function. + + +.. autofunction:: outbreak_data.get_outbreak_data + + + + + + + diff --git a/_sources/prevalence_by_location.rst.txt b/_sources/prevalence_by_location.rst.txt new file mode 100644 index 0000000..74c8c54 --- /dev/null +++ b/_sources/prevalence_by_location.rst.txt @@ -0,0 +1,69 @@ +prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None, lineage_crumbs=False) +------------------------------------------------------------------------------------------------------------------------------- + +.. autofunction:: outbreak_data.prevalence_by_location + +Example usage: + +1. Get the daily prevalence of lineage 'BA.2' in India since first detection:: + + df1 = od.daily_prev('ba.2', "IND") + print(df1) + +.. code-block:: + :caption: Output + + date total_count lineage_count total_count_rolling \ + 0 2020-08-01 39 1 29.000000 + 1 2020-08-02 100 0 41.285714 + 2 2020-08-03 38 0 42.000000 + 3 2020-08-04 20 0 42.285714 + 4 2020-08-05 26 0 36.000000 + ... ... ... ... ... + 1017 2023-05-15 2 0 5.857143 + 1018 2023-05-16 3 0 5.142857 + 1019 2023-05-17 3 0 3.285714 + 1020 2023-05-18 2 0 3.142857 + 1021 2023-05-20 1 0 2.000000 + + lineage_count_rolling proportion proportion_ci_lower \ + 0 0.142857 0.004926 0.000017 + 1 0.142857 0.003460 0.000012 + 2 0.142857 0.003401 0.000012 + 3 0.142857 0.003378 0.000012 + 4 0.142857 0.003968 0.000014 + ... ... ... ... + 1017 0.000000 0.000000 0.000078 + 1018 0.000000 0.000000 0.000093 + 1019 0.000000 0.000000 0.000151 + 1020 0.000000 0.000000 0.000151 + 1021 0.000000 0.000000 0.000217 + + proportion_ci_upper + 0 0.082286 + 1 0.059076 + 2 0.057719 + 3 0.057719 + 4 0.066944 + ... ... + 1017 0.330389 + 1018 0.379377 + 1019 0.535583 + 1020 0.535583 + 1021 0.666822 + +2. Get a cumulative summary of information regarding 'BA.2' in India:: + + df2 = od.daily_prev('ba.2', "IND", cumulative = True) + print(df2) + +.. code-block:: + :caption: Output + + Values + first_detected 2020-08-01 + global_prevalence 0.109641 + last_detected 2023-04-26 + lineage_count 25561 + total_count 233134 + diff --git a/_sources/seq_counts.rst.txt b/_sources/seq_counts.rst.txt new file mode 100644 index 0000000..91764de --- /dev/null +++ b/_sources/seq_counts.rst.txt @@ -0,0 +1,40 @@ +sequence_counts(location, cumulative, sub_admin) +------------------------------------------------- + +.. autofunction:: outbreak_data.sequence_counts + +Example usage: + +1. Get number of daily sequence counts in the US:: + + df = od.sequence_counts('USA') + print(df) + + +.. code-block:: + :caption: Output + + Key Values + 0 mutation ORF1b:P314L + 1 alt_codon CTT + 2 is_synonymous False + 3 codon_num 314 + 4 ref_codon CCT + 5 gene ORF1b + 6 pos 14407 + 7 alt_aa L + 8 ref_aa P + 9 type substitution + +2. Get total number of sequence counts + + df = od.sequence_counts('USA', cumulative=True) + print(df) + +.. code-block:: + :caption: Output + + Values + total_count 4617418 + + diff --git a/_sources/submission_date.rst.txt b/_sources/submission_date.rst.txt new file mode 100644 index 0000000..d4dde91 --- /dev/null +++ b/_sources/submission_date.rst.txt @@ -0,0 +1,16 @@ +submission_date(pango_lin, mutations=None, location) +---------------------------------------------------- + +.. autofunction:: outbreak_data.submission_date + +Example usage:: + + df = outbreak_data.submission_date('xbb.1', location='USA') + print(df) + +.. code-block:: + :caption: Output + + Values + date 2023-06-16 + date_count 5 diff --git a/_sources/wildcard_lineage.rst.txt b/_sources/wildcard_lineage.rst.txt new file mode 100644 index 0000000..cee40d8 --- /dev/null +++ b/_sources/wildcard_lineage.rst.txt @@ -0,0 +1,5 @@ +wildcard_lineage(name) +----------------------- + +.. autofunction:: outbreak_data.wildcard_lineage + diff --git a/_sources/wildcard_location.rst.txt b/_sources/wildcard_location.rst.txt new file mode 100644 index 0000000..bf2e495 --- /dev/null +++ b/_sources/wildcard_location.rst.txt @@ -0,0 +1,4 @@ +wildcard_location(name) +------------------------ + +.. autofunction:: outbreak_data.wildcard_location diff --git a/_sources/wildcard_mutations.rst.txt b/_sources/wildcard_mutations.rst.txt new file mode 100644 index 0000000..301323c --- /dev/null +++ b/_sources/wildcard_mutations.rst.txt @@ -0,0 +1,4 @@ +wildcard_mutations(name) +------------------------ + +.. autofunction:: outbreak_data.wildcard_mutations diff --git a/_static/_sphinx_javascript_frameworks_compat.js b/_static/_sphinx_javascript_frameworks_compat.js new file mode 100644 index 0000000..8141580 --- /dev/null +++ b/_static/_sphinx_javascript_frameworks_compat.js @@ -0,0 +1,123 @@ +/* Compatability shim for jQuery and underscores.js. + * + * Copyright Sphinx contributors + * Released under the two clause BSD licence + */ + +/** + * small helper function to urldecode strings + * + * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL + */ +jQuery.urldecode = function(x) { + if (!x) { + return x + } + return decodeURIComponent(x.replace(/\+/g, ' ')); +}; + +/** + * small helper function to urlencode strings + */ +jQuery.urlencode = encodeURIComponent; + +/** + * This function returns the parsed url parameters of the + * current request. 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b/_static/custom.css @@ -0,0 +1,274 @@ +/** + + CHANGES FOR CUSTOM.CSS SHOULD BE MADE INSIDE CUSTOM.SCSS + + + + Requirements: + + - pip install compile-scss https://pypi.org/project/compile-scss/ + + + +To make changes to styling, first run the following in the root of the project: + + - pip install -e .[dev] + + + +Then you can edit and make changes to this file and see the results by doing the following: + + Steps: + + - Run: compile_scss --watch from inside /renku_sphinx_theme + + - That command will compile scss changes into css. + + - After doing changes commit scss and css files. + +*/ +.wy-nav-side { + background: #01192d; +} + +@media screen and (min-width: 1100px) { + .wy-nav-content-wrap { + background:#01192d; + } +} + +a { + color: #009568; +} + +a:hover { + color: #00bd84; +} + +a:visited { + color: #009568; +} + +.rst-content { + color: #3d3d3d; +} + +.rst-content code.literal { + color: #d26a98; +} + +.rst-content tt.literal { + color: #d26a98; +} + +.rst-content .note { + color: #003274; + background: #ccddf3; + padding: 1rem; + margin-bottom: 1rem; +} + +.rst-content .note .admonition-title { + display: none; +} + +.rst-content .warning { + color: #605000; + background: #fcf4cc; + padding: 1rem; + margin-bottom: 1rem; +} + +.rst-content .warning .admonition-title { + display: none; +} + +.rst-content .highlight { + background: #f5f5f5; +} + +.wy-side-scroll { + background-color: #01192d; +} + +.wy-side-nav-search { + background-color: #01192d; +} + +.wy-side-nav-search input[type="text"] { + width: 100%; + border-radius: 0px; + padding: 6px 12px; + border-color: #01192d; +} + +.wy-menu-vertical a { + font-size: 100%; + color: #d9d9d9; + padding-top: 0.6rem; + padding-bottom: 0.6rem; + background-color: inherit; +} + +.wy-menu-vertical a:hover { + background-color: unset; + opacity: 1; +} + +.wy-menu-vertical li.current > a { + background-color: #01192d; + color: white; +} + +.wy-menu-vertical li.current > a span.toctree-expand { + display: block; + font-size: inherit; + line-height: inherit; + color: inherit; +} + +.wy-menu-vertical li.current > a span.toctree-expand:before { + display: block; + font-size: inherit; + line-height: inherit; + color: inherit; +} + +.wy-menu-vertical li.current > a span.toctree-expand:hover { + color: white; +} + +.wy-menu-vertical li.current > a:hover { + background-color: #01192d; + color: white; +} + +.wy-menu-vertical li.current > a:hover span.toctree-expand { + color: white; +} + +.wy-menu-vertical .toctree-l1 { + opacity: 0.5; +} + +.wy-menu-vertical .toctree-l1:hover { + opacity: 1; + background-color: inherit; +} + +.wy-menu-vertical li.toctree-l1.current { + opacity: 1; + background-color: inherit; +} + +.wy-menu-vertical li.toctree-l1.current > a { + border: 0px; +} + +.wy-menu-vertical .toctree-l2:hover { + background-color: #566673; +} + +.wy-menu-vertical li.toctree-l2.current > a { + background-color: #566673; + color: white; +} + +.wy-menu-vertical li.toctree-l2.current li.toctree-l3 > a { + background-color: #e4e7ea; + color: #838383; +} + +.wy-menu-vertical li.toctree-l2.current li.toctree-l3 > a:hover { + color: #3d3d3d; +} + +.wy-menu-vertical li.toctree-l2.current li.toctree-l3 > a:hover span.toctree-expand { + color: #3d3d3d; +} + +.wy-menu-vertical li.toctree-l2.current li.toctree-l3.current > a { + color: #3d3d3d; +} + +.wy-menu-vertical li.toctree-l2 a { + border: 0px; + background-color: #566673; + color: #d9d9d9; +} + +.wy-menu-vertical li.toctree-l2 a span.toctree-expand { + display: block; + font-size: inherit; + line-height: inherit; + color: inherit; +} + +.wy-menu-vertical li.toctree-l2 a span.toctree-expand:before { + display: block; + font-size: inherit; + line-height: inherit; + color: inherit; +} + +.wy-menu-vertical li.toctree-l2 a span.toctree-expand:hover { + color: white; +} + +.wy-menu-vertical li.toctree-l2 a:hover { + color: white; + background-color: #566673; +} + +.wy-menu-vertical li.toctree-l2 a:hover span.toctree-expand { + color: white; +} + +.wy-menu-vertical li.toctree-l3.current > a { + background-color: #e4e7ea; + color: #838383; +} + +.wy-menu-vertical li.toctree-l3.current li.toctree-l4 > a { + background-color: #e4e7ea; + color: #838383; +} + +.wy-menu-vertical li.toctree-l3.current li.toctree-l4.current > a { + color: #3d3d3d; +} + +.wy-nav-top { + background-color: #01192d; +} + +.btn { + display: inline-block; + font-weight: 400; + line-height: 1.5; + color: #3d3d3d; + text-align: center; + text-decoration: none; + vertical-align: middle; + cursor: pointer; + -webkit-user-select: none; + -ms-user-select: none; + user-select: none; + background-color: transparent; + border: 1px solid transparent; + padding: 0.375rem 0.75rem; + font-size: 1rem; + border-radius: 0; + transition: color 0.15s ease-in-out, background-color 0.15s ease-in-out, border-color 0.15s ease-in-out, box-shadow 0.15s ease-in-out; + box-shadow: unset; +} + +.btn-neutral { + background: unset !important; + color: #838383 !important; +} + +.btn-neutral:active { + padding: 0.375rem 0.75rem; + box-shadow: unset; +} diff --git a/_static/custom.scss b/_static/custom.scss new file mode 100644 index 0000000..035b16a --- /dev/null +++ b/_static/custom.scss @@ -0,0 +1,292 @@ +/** + CHANGES FOR CUSTOM.CSS SHOULD BE MADE INSIDE CUSTOM.SCSS + + Requirements: + - pip install compile-scss https://pypi.org/project/compile-scss/ + +To make changes to styling, first run the following in the root of the project: + - pip install -e .[dev] + +Then you can edit and make changes to this file and see the results by doing the following: + Steps: + - Run: compile_scss --watch from inside /renku_sphinx_theme + - That command will compile scss changes into css. + - After doing changes commit scss and css files. +*/ + +$rk-blue: #01192d; +$rk-green: #009568; +$rk-green-lighter: hsl(162, 100%, 37%); +$rk-background: #f5f5f5; +$rk-white: #f5f5f5; +$rk-dark: #3d3d3d; +$rk-warning-background: #fcf4cc; +$rk-warning-font: #605000; +$rk-info-background: #ccddf3; +$rk-info-font: #003274; +$rk-light-blue: #566673; +$rk-gray: #838383; +$rk-light-gray: #e4e7ea; +$rk-pink: #d26a98; + +//side background +.wy-nav-side { + background: $rk-blue; +} + +@media screen and (min-width: 1100px) { + .wy-nav-content-wrap { + background:$rk-blue; + } +} + +//all links are green +a { + color: $rk-green; + &:hover { + color: $rk-green-lighter; + } + &:visited { + color: $rk-green; + } +} + +// right content -- docs +.rst-content { + color: $rk-dark; + + // code color + code.literal { + color: $rk-pink; + } + + tt.literal { + color: $rk-pink; + } + + // note style + .note { + .admonition-title { + display: none; + } + color: $rk-info-font; + background: $rk-info-background; + padding: 1rem; + margin-bottom: 1rem; + } + + // warning style + .warning { + .admonition-title { + display: none; + } + color: $rk-warning-font; + background: $rk-warning-background; + padding: 1rem; + margin-bottom: 1rem; + } + + // code blocks + .highlight { + background: $rk-background; + } +} + +// menu background +.wy-side-scroll { + background-color: $rk-blue; +} + +// side nav +.wy-side-nav-search { + background-color: $rk-blue; + input[type="text"] { + width: 100%; + border-radius: 0px; + padding: 6px 12px; + border-color: $rk-blue; + } +} + +// Vertical menu +.wy-menu-vertical { + a { + font-size: 100%; + color: #d9d9d9; + padding-top: 0.6rem; + padding-bottom: 0.6rem; + background-color: inherit; + &:hover { + background-color: unset; + opacity: 1; + } + } + + // all links inside the menu + li.current { + > a { + background-color: $rk-blue; + color: white; + span.toctree-expand { + display: block; + font-size: inherit; + line-height: inherit; + color: inherit; + &:before { + display: block; + font-size: inherit; + line-height: inherit; + color: inherit; + } + &:hover { + color: white; + } + } + &:hover { + background-color: $rk-blue; + color: white; + span.toctree-expand { + color: white; + } + } + } + } + + // level 1 link + .toctree-l1 { + opacity: 0.5; + &:hover { + opacity: 1; + background-color: inherit; + } + } + + // selected level 1 link + li.toctree-l1.current { + opacity: 1; + background-color: inherit; + > a { + border: 0px; + } + } + + .toctree-l2 { + &:hover { + background-color: #566673; + } + } + + li.toctree-l2.current { + > a { + background-color: $rk-light-blue; + color: white; + } + li.toctree-l3 { + > a { + background-color: $rk-light-gray; + color: $rk-gray; + &:hover { + color: $rk-dark; + span.toctree-expand { + color: $rk-dark; + } + } + } + } + li.toctree-l3.current { + > a { + color: $rk-dark; + } + } + } + + li.toctree-l2 { + a { + border: 0px; + background-color: $rk-light-blue; + color: #d9d9d9; + // + span.toctree-expand { + display: block; + font-size: inherit; + line-height: inherit; + color: inherit; + &:before { + display: block; + font-size: inherit; + line-height: inherit; + color: inherit; + } + &:hover { + color: white; + } + } + // + &:hover { + color: white; + background-color: $rk-light-blue; + /// + span.toctree-expand { + color: white; + } + /// + } + } + } + + li.toctree-l3.current { + > a { + background-color: $rk-light-gray; + color: $rk-gray; + } + li.toctree-l4 { + > a { + background-color: $rk-light-gray; + color: $rk-gray; + } + &.current { + > a { + color: $rk-dark; + } + } + } + } +} + +// Responsive small navigation +.wy-nav-top { + background-color: $rk-blue; +} + +// Button +.btn { + display: inline-block; + font-weight: 400; + line-height: 1.5; + color: $rk-dark; + text-align: center; + text-decoration: none; + vertical-align: middle; + cursor: pointer; + -webkit-user-select: none; + -ms-user-select: none; + user-select: none; + background-color: transparent; + border: 1px solid transparent; + padding: 0.375rem 0.75rem; + font-size: 1rem; + border-radius: 0; + transition: color 0.15s ease-in-out, background-color 0.15s ease-in-out, + border-color 0.15s ease-in-out, box-shadow 0.15s ease-in-out; + box-shadow: unset; +} + +// Neutral button - prev next +.btn-neutral { + background: unset !important; + color: $rk-gray !important; + &:active { + padding: 0.375rem 0.75rem; + box-shadow: unset; + } +} diff --git a/_static/doctools.js b/_static/doctools.js new file mode 100644 index 0000000..d06a71d --- /dev/null +++ b/_static/doctools.js @@ -0,0 +1,156 @@ +/* + * doctools.js + * ~~~~~~~~~~~ + * + * Base JavaScript utilities for all Sphinx HTML documentation. + * + * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS. + * :license: BSD, see LICENSE for details. + * + */ +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); + } +}; + +/** + * Small JavaScript module for the documentation. + */ +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); + }, + + /** + * i18n support + */ + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", + + // gettext and ngettext don't access this so that the functions + // can safely bound to a different name (_ = Documentation.gettext) + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } + }, + + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; + }, + + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; + }, + + /** + * helper function to focus on search bar + */ + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); + }, + + /** + * Initialise the domain index toggle buttons + */ + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); + } + }; + + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); + }, + + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); + } + break; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); + } + break; + } + } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } + }); + }, +}; + +// quick alias for translations +const _ = Documentation.gettext; + +_ready(Documentation.init); diff --git a/_static/documentation_options.js b/_static/documentation_options.js new file mode 100644 index 0000000..e21c068 --- /dev/null +++ b/_static/documentation_options.js @@ -0,0 +1,13 @@ +const DOCUMENTATION_OPTIONS = { + VERSION: '0.1', + LANGUAGE: 'en', + COLLAPSE_INDEX: false, + BUILDER: 'html', + FILE_SUFFIX: '.html', + LINK_SUFFIX: '.html', + HAS_SOURCE: true, + SOURCELINK_SUFFIX: '.txt', + NAVIGATION_WITH_KEYS: false, + SHOW_SEARCH_SUMMARY: true, + ENABLE_SEARCH_SHORTCUTS: true, +}; \ No newline at end of file diff --git a/_static/favicon.png b/_static/favicon.png new file mode 100644 index 0000000..948a9b2 Binary files /dev/null and b/_static/favicon.png differ diff --git a/_static/file.png b/_static/file.png new file mode 100644 index 0000000..a858a41 Binary files /dev/null and b/_static/file.png differ diff --git a/_static/fonts.css b/_static/fonts.css new file mode 100644 index 0000000..a7acf06 --- /dev/null +++ b/_static/fonts.css @@ -0,0 +1,41 @@ +/* Webfont: Calcutta-Bold */ +@import url("https://fonts.googleapis.com/css2?family=Source+Code+Pro:ital,wght@0,400;0,500;1,400&display=swap"); +@font-face { + font-family: 'Calcutta'; + src: url("fonts/calcutta/Calcutta-Bold.eot"); + /* IE9 Compat Modes */ + src: url("fonts/calcutta/Calcutta-Bold.eot?#iefix") format("embedded-opentype"), url("fonts/calcutta/Calcutta-Bold.woff") format("woff"), url("fonts/calcutta/Calcutta-Bold.ttf") format("truetype"), url("fonts/calcutta/Calcutta-Bold.svg#Calcutta-Bold") format("svg"); + /* Legacy iOS */ + font-style: 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b/_static/fonts/fontawesome-webfont.svg @@ -0,0 +1,2671 @@ + + + + +Created by FontForge 20120731 at Mon Oct 24 17:37:40 2016 + By ,,, +Copyright Dave Gandy 2016. 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But as of jQuery 3.0 (2016), strict mode should be common +// enough that all such attempts are guarded in a try block. +"use strict"; + +var arr = []; + +var getProto = Object.getPrototypeOf; + +var slice = arr.slice; + +var flat = arr.flat ? function( array ) { + return arr.flat.call( array ); +} : function( array ) { + return arr.concat.apply( [], array ); +}; + + +var push = arr.push; + +var indexOf = arr.indexOf; + +var class2type = {}; + +var toString = class2type.toString; + +var hasOwn = class2type.hasOwnProperty; + +var fnToString = hasOwn.toString; + +var ObjectFunctionString = fnToString.call( Object ); + +var support = {}; + +var isFunction = function isFunction( obj ) { + + // Support: Chrome <=57, Firefox <=52 + // In some browsers, typeof returns "function" for HTML elements + // (i.e., `typeof document.createElement( "object" ) === "function"`). + // We don't want to classify *any* DOM node as a function. + return typeof obj === "function" && typeof obj.nodeType !== "number"; + }; + + +var isWindow = function isWindow( obj ) { + return obj != null && obj === obj.window; + }; + + +var document = window.document; + + + + var preservedScriptAttributes = { + type: true, + src: true, + nonce: true, + noModule: true + }; + + function DOMEval( code, node, doc ) { + doc = doc || document; + + var i, val, + script = doc.createElement( "script" ); + + script.text = code; + if ( node ) { + for ( i in preservedScriptAttributes ) { + + // Support: Firefox 64+, Edge 18+ + // Some browsers don't support the "nonce" property on scripts. + // On the other hand, just using `getAttribute` is not enough as + // the `nonce` attribute is reset to an empty string whenever it + // becomes browsing-context connected. + // See https://github.com/whatwg/html/issues/2369 + // See https://html.spec.whatwg.org/#nonce-attributes + // The `node.getAttribute` check was added for the sake of + // `jQuery.globalEval` so that it can fake a nonce-containing node + // via an object. + val = node[ i ] || node.getAttribute && node.getAttribute( i ); + if ( val ) { + script.setAttribute( i, val ); + } + } + } + doc.head.appendChild( script ).parentNode.removeChild( script ); + } + + +function toType( obj ) { + if ( obj == null ) { + return obj + ""; + } + + // Support: Android <=2.3 only (functionish RegExp) + return typeof obj === "object" || typeof obj === "function" ? + class2type[ toString.call( obj ) ] || "object" : + typeof obj; +} +/* global Symbol */ +// Defining this global in .eslintrc.json would create a danger of using the global +// unguarded in another place, it seems safer to define global only for this module + + + +var + version = "3.5.1", + + // Define a local copy of jQuery + jQuery = function( selector, context ) { + + // The jQuery object is actually just the init constructor 'enhanced' + // Need init if jQuery is called (just allow error to be thrown if not included) + return new jQuery.fn.init( selector, context ); + }; + +jQuery.fn = jQuery.prototype = { + + // The current version of jQuery being used + jquery: version, + + constructor: jQuery, + + // The default length of a jQuery object is 0 + length: 0, + + toArray: function() { + return slice.call( this ); + }, + + // Get the Nth element in the matched element set OR + // Get the whole matched element set as a clean array + get: function( num ) { + + // Return all the elements in a clean array + if ( num == null ) { + return slice.call( this ); + } + + // Return just the one element from the set + return num < 0 ? this[ num + this.length ] : this[ num ]; + }, + + // Take an array of elements and push it onto the stack + // (returning the new matched element set) + pushStack: function( elems ) { + + // Build a new jQuery matched element set + var ret = jQuery.merge( this.constructor(), elems ); + + // Add the old object onto the stack (as a reference) + ret.prevObject = this; + + // Return the newly-formed element set + return ret; + }, + + // Execute a callback for every element in the matched set. + each: function( callback ) { + return jQuery.each( this, callback ); + }, + + map: function( callback ) { + return this.pushStack( jQuery.map( this, function( elem, i ) { + return callback.call( elem, i, elem ); + } ) ); + }, + + slice: function() { + return this.pushStack( slice.apply( this, arguments ) ); + }, + + first: function() { + return this.eq( 0 ); + }, + + last: function() { + return this.eq( -1 ); + }, + + even: function() { + return this.pushStack( jQuery.grep( this, function( _elem, i ) { + return ( i + 1 ) % 2; + } ) ); + }, + + odd: function() { + return this.pushStack( jQuery.grep( this, function( _elem, i ) { + return i % 2; + } ) ); + }, + + eq: function( i ) { + var len = this.length, + j = +i + ( i < 0 ? len : 0 ); + return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] ); + }, + + end: function() { + return this.prevObject || this.constructor(); + }, + + // For internal use only. + // Behaves like an Array's method, not like a jQuery method. + push: push, + sort: arr.sort, + splice: arr.splice +}; + +jQuery.extend = jQuery.fn.extend = function() { + var options, name, src, copy, copyIsArray, clone, + target = arguments[ 0 ] || {}, + i = 1, + length = arguments.length, + deep = false; + + // Handle a deep copy situation + if ( typeof target === "boolean" ) { + deep = target; + + // Skip the boolean and the target + target = arguments[ i ] || {}; + i++; + } + + // Handle case when target is a string or something (possible in deep copy) + if ( typeof target !== "object" && !isFunction( target ) ) { + target = {}; + } + + // Extend jQuery itself if only one argument is passed + if ( i === length ) { + target = this; + i--; + } + + for ( ; i < length; i++ ) { + + // Only deal with non-null/undefined values + if ( ( options = arguments[ i ] ) != null ) { + + // Extend the base object + for ( name in options ) { + copy = options[ name ]; + + // Prevent Object.prototype pollution + // Prevent never-ending loop + if ( name === "__proto__" || target === copy ) { + continue; + } + + // Recurse if we're merging plain objects or arrays + if ( deep && copy && ( jQuery.isPlainObject( copy ) || + ( copyIsArray = Array.isArray( copy ) ) ) ) { + src = target[ name ]; + + // Ensure proper type for the source value + if ( copyIsArray && !Array.isArray( src ) ) { + clone = []; + } else if ( !copyIsArray && !jQuery.isPlainObject( src ) ) { + clone = {}; + } else { + clone = src; + } + copyIsArray = false; + + // Never move original objects, clone them + target[ name ] = jQuery.extend( deep, clone, copy ); + + // Don't bring in undefined values + } else if ( copy !== undefined ) { + target[ name ] = copy; + } + } + } + } + + // Return the modified object + return target; +}; + +jQuery.extend( { + + // Unique for each copy of jQuery on the page + expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), + + // Assume jQuery is ready without the ready module + isReady: true, + + error: function( msg ) { + throw new Error( msg ); + }, + + noop: function() {}, + + isPlainObject: function( obj ) { + var proto, Ctor; + + // Detect obvious negatives + // Use toString instead of jQuery.type to catch host objects + if ( !obj || toString.call( obj ) !== "[object Object]" ) { + return false; + } + + proto = getProto( obj ); + + // Objects with no prototype (e.g., `Object.create( null )`) are plain + if ( !proto ) { + return true; + } + + // Objects with prototype are plain iff they were constructed by a global Object function + Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor; + return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString; + }, + + isEmptyObject: function( obj ) { + var name; + + for ( name in obj ) { + return false; + } + return true; + }, + + // Evaluates a script in a provided context; falls back to the global one + // if not specified. + globalEval: function( code, options, doc ) { + DOMEval( code, { nonce: options && options.nonce }, doc ); + }, + + each: function( obj, callback ) { + var length, i = 0; + + if ( isArrayLike( obj ) ) { + length = obj.length; + for ( ; i < length; i++ ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } else { + for ( i in obj ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } + + return obj; + }, + + // results is for internal usage only + makeArray: function( arr, results ) { + var ret = results || []; + + if ( arr != null ) { + if ( isArrayLike( Object( arr ) ) ) { + jQuery.merge( ret, + typeof arr === "string" ? + [ arr ] : arr + ); + } else { + push.call( ret, arr ); + } + } + + return ret; + }, + + inArray: function( elem, arr, i ) { + return arr == null ? -1 : indexOf.call( arr, elem, i ); + }, + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + merge: function( first, second ) { + var len = +second.length, + j = 0, + i = first.length; + + for ( ; j < len; j++ ) { + first[ i++ ] = second[ j ]; + } + + first.length = i; + + return first; + }, + + grep: function( elems, callback, invert ) { + var callbackInverse, + matches = [], + i = 0, + length = elems.length, + callbackExpect = !invert; + + // Go through the array, only saving the items + // that pass the validator function + for ( ; i < length; i++ ) { + callbackInverse = !callback( elems[ i ], i ); + if ( callbackInverse !== callbackExpect ) { + matches.push( elems[ i ] ); + } + } + + return matches; + }, + + // arg is for internal usage only + map: function( elems, callback, arg ) { + var length, value, + i = 0, + ret = []; + + // Go through the array, translating each of the items to their new values + if ( isArrayLike( elems ) ) { + length = elems.length; + for ( ; i < length; i++ ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + + // Go through every key on the object, + } else { + for ( i in elems ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + } + + // Flatten any nested arrays + return flat( ret ); + }, + + // A global GUID counter for objects + guid: 1, + + // jQuery.support is not used in Core but other projects attach their + // properties to it so it needs to exist. + support: support +} ); + +if ( typeof Symbol === "function" ) { + jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ]; +} + +// Populate the class2type map +jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ), +function( _i, name ) { + class2type[ "[object " + name + "]" ] = name.toLowerCase(); +} ); + +function isArrayLike( obj ) { + + // Support: real iOS 8.2 only (not reproducible in simulator) + // `in` check used to prevent JIT error (gh-2145) + // hasOwn isn't used here due to false negatives + // regarding Nodelist length in IE + var length = !!obj && "length" in obj && obj.length, + type = toType( obj ); + + if ( isFunction( obj ) || isWindow( obj ) ) { + return false; + } + + return type === "array" || length === 0 || + typeof length === "number" && length > 0 && ( length - 1 ) in obj; +} +var Sizzle = +/*! + * Sizzle CSS Selector Engine v2.3.5 + * https://sizzlejs.com/ + * + * Copyright JS Foundation and other contributors + * Released under the MIT license + * https://js.foundation/ + * + * Date: 2020-03-14 + */ +( function( window ) { +var i, + support, + Expr, + getText, + isXML, + tokenize, + compile, + select, + outermostContext, + sortInput, + hasDuplicate, + + // Local document vars + setDocument, + document, + docElem, + documentIsHTML, + rbuggyQSA, + rbuggyMatches, + matches, + contains, + + // Instance-specific data + expando = "sizzle" + 1 * new Date(), + preferredDoc = window.document, + dirruns = 0, + done = 0, + classCache = createCache(), + tokenCache = createCache(), + compilerCache = createCache(), + nonnativeSelectorCache = createCache(), + sortOrder = function( a, b ) { + if ( a === b ) { + hasDuplicate = true; + } + return 0; + }, + + // Instance methods + hasOwn = ( {} ).hasOwnProperty, + arr = [], + pop = arr.pop, + pushNative = arr.push, + push = arr.push, + slice = arr.slice, + + // Use a stripped-down indexOf as it's faster than native + // https://jsperf.com/thor-indexof-vs-for/5 + indexOf = function( list, elem ) { + var i = 0, + len = list.length; + for ( ; i < len; i++ ) { + if ( list[ i ] === elem ) { + return i; + } + } + return -1; + }, + + booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|" + + "ismap|loop|multiple|open|readonly|required|scoped", + + // Regular expressions + + // http://www.w3.org/TR/css3-selectors/#whitespace + whitespace = "[\\x20\\t\\r\\n\\f]", + + // https://www.w3.org/TR/css-syntax-3/#ident-token-diagram + identifier = "(?:\\\\[\\da-fA-F]{1,6}" + whitespace + + "?|\\\\[^\\r\\n\\f]|[\\w-]|[^\0-\\x7f])+", + + // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors + attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + + + // Operator (capture 2) + "*([*^$|!~]?=)" + whitespace + + + // "Attribute values must be CSS identifiers [capture 5] + // or strings [capture 3 or capture 4]" + "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + + whitespace + "*\\]", + + pseudos = ":(" + identifier + ")(?:\\((" + + + // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: + // 1. quoted (capture 3; capture 4 or capture 5) + "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + + + // 2. simple (capture 6) + "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + + + // 3. anything else (capture 2) + ".*" + + ")\\)|)", + + // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter + rwhitespace = new RegExp( whitespace + "+", "g" ), + rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + + whitespace + "+$", "g" ), + + rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), + rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + + "*" ), + rdescend = new RegExp( whitespace + "|>" ), + + rpseudo = new RegExp( pseudos ), + ridentifier = new RegExp( "^" + identifier + "$" ), + + matchExpr = { + "ID": new RegExp( "^#(" + identifier + ")" ), + "CLASS": new RegExp( "^\\.(" + identifier + ")" ), + "TAG": new RegExp( "^(" + identifier + "|[*])" ), + "ATTR": new RegExp( "^" + attributes ), + "PSEUDO": new RegExp( "^" + pseudos ), + "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + + whitespace + "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + + whitespace + "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), + "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), + + // For use in libraries implementing .is() + // We use this for POS matching in `select` + "needsContext": new RegExp( "^" + whitespace + + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + whitespace + + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) + }, + + rhtml = /HTML$/i, + rinputs = /^(?:input|select|textarea|button)$/i, + rheader = /^h\d$/i, + + rnative = /^[^{]+\{\s*\[native \w/, + + // Easily-parseable/retrievable ID or TAG or CLASS selectors + rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, + + rsibling = /[+~]/, + + // CSS escapes + // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters + runescape = new RegExp( "\\\\[\\da-fA-F]{1,6}" + whitespace + "?|\\\\([^\\r\\n\\f])", "g" ), + funescape = function( escape, nonHex ) { + var high = "0x" + escape.slice( 1 ) - 0x10000; + + return nonHex ? + + // Strip the backslash prefix from a non-hex escape sequence + nonHex : + + // Replace a hexadecimal escape sequence with the encoded Unicode code point + // Support: IE <=11+ + // For values outside the Basic Multilingual Plane (BMP), manually construct a + // surrogate pair + high < 0 ? + String.fromCharCode( high + 0x10000 ) : + String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); + }, + + // CSS string/identifier serialization + // https://drafts.csswg.org/cssom/#common-serializing-idioms + rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g, + fcssescape = function( ch, asCodePoint ) { + if ( asCodePoint ) { + + // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER + if ( ch === "\0" ) { + return "\uFFFD"; + } + + // Control characters and (dependent upon position) numbers get escaped as code points + return ch.slice( 0, -1 ) + "\\" + + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " "; + } + + // Other potentially-special ASCII characters get backslash-escaped + return "\\" + ch; + }, + + // Used for iframes + // See setDocument() + // Removing the function wrapper causes a "Permission Denied" + // error in IE + unloadHandler = function() { + setDocument(); + }, + + inDisabledFieldset = addCombinator( + function( elem ) { + return elem.disabled === true && elem.nodeName.toLowerCase() === "fieldset"; + }, + { dir: "parentNode", next: "legend" } + ); + +// Optimize for push.apply( _, NodeList ) +try { + push.apply( + ( arr = slice.call( preferredDoc.childNodes ) ), + preferredDoc.childNodes + ); + + // Support: Android<4.0 + // Detect silently failing push.apply + // eslint-disable-next-line no-unused-expressions + arr[ preferredDoc.childNodes.length ].nodeType; +} catch ( e ) { + push = { apply: arr.length ? + + // Leverage slice if possible + function( target, els ) { + pushNative.apply( target, slice.call( els ) ); + } : + + // Support: IE<9 + // Otherwise append directly + function( target, els ) { + var j = target.length, + i = 0; + + // Can't trust NodeList.length + while ( ( target[ j++ ] = els[ i++ ] ) ) {} + target.length = j - 1; + } + }; +} + +function Sizzle( selector, context, results, seed ) { + var m, i, elem, nid, match, groups, newSelector, + newContext = context && context.ownerDocument, + + // nodeType defaults to 9, since context defaults to document + nodeType = context ? context.nodeType : 9; + + results = results || []; + + // Return early from calls with invalid selector or context + if ( typeof selector !== "string" || !selector || + nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { + + return results; + } + + // Try to shortcut find operations (as opposed to filters) in HTML documents + if ( !seed ) { + setDocument( context ); + context = context || document; + + if ( documentIsHTML ) { + + // If the selector is sufficiently simple, try using a "get*By*" DOM method + // (excepting DocumentFragment context, where the methods don't exist) + if ( nodeType !== 11 && ( match = rquickExpr.exec( selector ) ) ) { + + // ID selector + if ( ( m = match[ 1 ] ) ) { + + // Document context + if ( nodeType === 9 ) { + if ( ( elem = context.getElementById( m ) ) ) { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( elem.id === m ) { + results.push( elem ); + return results; + } + } else { + return results; + } + + // Element context + } else { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( newContext && ( elem = newContext.getElementById( m ) ) && + contains( context, elem ) && + elem.id === m ) { + + results.push( elem ); + return results; + } + } + + // Type selector + } else if ( match[ 2 ] ) { + push.apply( results, context.getElementsByTagName( selector ) ); + return results; + + // Class selector + } else if ( ( m = match[ 3 ] ) && support.getElementsByClassName && + context.getElementsByClassName ) { + + push.apply( results, context.getElementsByClassName( m ) ); + return results; + } + } + + // Take advantage of querySelectorAll + if ( support.qsa && + !nonnativeSelectorCache[ selector + " " ] && + ( !rbuggyQSA || !rbuggyQSA.test( selector ) ) && + + // Support: IE 8 only + // Exclude object elements + ( nodeType !== 1 || context.nodeName.toLowerCase() !== "object" ) ) { + + newSelector = selector; + newContext = context; + + // qSA considers elements outside a scoping root when evaluating child or + // descendant combinators, which is not what we want. + // In such cases, we work around the behavior by prefixing every selector in the + // list with an ID selector referencing the scope context. + // The technique has to be used as well when a leading combinator is used + // as such selectors are not recognized by querySelectorAll. + // Thanks to Andrew Dupont for this technique. + if ( nodeType === 1 && + ( rdescend.test( selector ) || rcombinators.test( selector ) ) ) { + + // Expand context for sibling selectors + newContext = rsibling.test( selector ) && testContext( context.parentNode ) || + context; + + // We can use :scope instead of the ID hack if the browser + // supports it & if we're not changing the context. + if ( newContext !== context || !support.scope ) { + + // Capture the context ID, setting it first if necessary + if ( ( nid = context.getAttribute( "id" ) ) ) { + nid = nid.replace( rcssescape, fcssescape ); + } else { + context.setAttribute( "id", ( nid = expando ) ); + } + } + + // Prefix every selector in the list + groups = tokenize( selector ); + i = groups.length; + while ( i-- ) { + groups[ i ] = ( nid ? "#" + nid : ":scope" ) + " " + + toSelector( groups[ i ] ); + } + newSelector = groups.join( "," ); + } + + try { + push.apply( results, + newContext.querySelectorAll( newSelector ) + ); + return results; + } catch ( qsaError ) { + nonnativeSelectorCache( selector, true ); + } finally { + if ( nid === expando ) { + context.removeAttribute( "id" ); + } + } + } + } + } + + // All others + return select( selector.replace( rtrim, "$1" ), context, results, seed ); +} + +/** + * Create key-value caches of limited size + * @returns {function(string, object)} Returns the Object data after storing it on itself with + * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) + * deleting the oldest entry + */ +function createCache() { + var keys = []; + + function cache( key, value ) { + + // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) + if ( keys.push( key + " " ) > Expr.cacheLength ) { + + // Only keep the most recent entries + delete cache[ keys.shift() ]; + } + return ( cache[ key + " " ] = value ); + } + return cache; +} + +/** + * Mark a function for special use by Sizzle + * @param {Function} fn The function to mark + */ +function markFunction( fn ) { + fn[ expando ] = true; + return fn; +} + +/** + * Support testing using an element + * @param {Function} fn Passed the created element and returns a boolean result + */ +function assert( fn ) { + var el = document.createElement( "fieldset" ); + + try { + return !!fn( el ); + } catch ( e ) { + return false; + } finally { + + // Remove from its parent by default + if ( el.parentNode ) { + el.parentNode.removeChild( el ); + } + + // release memory in IE + el = null; + } +} + +/** + * Adds the same handler for all of the specified attrs + * @param {String} attrs Pipe-separated list of attributes + * @param {Function} handler The method that will be applied + */ +function addHandle( attrs, handler ) { + var arr = attrs.split( "|" ), + i = arr.length; + + while ( i-- ) { + Expr.attrHandle[ arr[ i ] ] = handler; + } +} + +/** + * Checks document order of two siblings + * @param {Element} a + * @param {Element} b + * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b + */ +function siblingCheck( a, b ) { + var cur = b && a, + diff = cur && a.nodeType === 1 && b.nodeType === 1 && + a.sourceIndex - b.sourceIndex; + + // Use IE sourceIndex if available on both nodes + if ( diff ) { + return diff; + } + + // Check if b follows a + if ( cur ) { + while ( ( cur = cur.nextSibling ) ) { + if ( cur === b ) { + return -1; + } + } + } + + return a ? 1 : -1; +} + +/** + * Returns a function to use in pseudos for input types + * @param {String} type + */ +function createInputPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for buttons + * @param {String} type + */ +function createButtonPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return ( name === "input" || name === "button" ) && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for :enabled/:disabled + * @param {Boolean} disabled true for :disabled; false for :enabled + */ +function createDisabledPseudo( disabled ) { + + // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable + return function( elem ) { + + // Only certain elements can match :enabled or :disabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled + if ( "form" in elem ) { + + // Check for inherited disabledness on relevant non-disabled elements: + // * listed form-associated elements in a disabled fieldset + // https://html.spec.whatwg.org/multipage/forms.html#category-listed + // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled + // * option elements in a disabled optgroup + // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled + // All such elements have a "form" property. + if ( elem.parentNode && elem.disabled === false ) { + + // Option elements defer to a parent optgroup if present + if ( "label" in elem ) { + if ( "label" in elem.parentNode ) { + return elem.parentNode.disabled === disabled; + } else { + return elem.disabled === disabled; + } + } + + // Support: IE 6 - 11 + // Use the isDisabled shortcut property to check for disabled fieldset ancestors + return elem.isDisabled === disabled || + + // Where there is no isDisabled, check manually + /* jshint -W018 */ + elem.isDisabled !== !disabled && + inDisabledFieldset( elem ) === disabled; + } + + return elem.disabled === disabled; + + // Try to winnow out elements that can't be disabled before trusting the disabled property. + // Some victims get caught in our net (label, legend, menu, track), but it shouldn't + // even exist on them, let alone have a boolean value. + } else if ( "label" in elem ) { + return elem.disabled === disabled; + } + + // Remaining elements are neither :enabled nor :disabled + return false; + }; +} + +/** + * Returns a function to use in pseudos for positionals + * @param {Function} fn + */ +function createPositionalPseudo( fn ) { + return markFunction( function( argument ) { + argument = +argument; + return markFunction( function( seed, matches ) { + var j, + matchIndexes = fn( [], seed.length, argument ), + i = matchIndexes.length; + + // Match elements found at the specified indexes + while ( i-- ) { + if ( seed[ ( j = matchIndexes[ i ] ) ] ) { + seed[ j ] = !( matches[ j ] = seed[ j ] ); + } + } + } ); + } ); +} + +/** + * Checks a node for validity as a Sizzle context + * @param {Element|Object=} context + * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value + */ +function testContext( context ) { + return context && typeof context.getElementsByTagName !== "undefined" && context; +} + +// Expose support vars for convenience +support = Sizzle.support = {}; + +/** + * Detects XML nodes + * @param {Element|Object} elem An element or a document + * @returns {Boolean} True iff elem is a non-HTML XML node + */ +isXML = Sizzle.isXML = function( elem ) { + var namespace = elem.namespaceURI, + docElem = ( elem.ownerDocument || elem ).documentElement; + + // Support: IE <=8 + // Assume HTML when documentElement doesn't yet exist, such as inside loading iframes + // https://bugs.jquery.com/ticket/4833 + return !rhtml.test( namespace || docElem && docElem.nodeName || "HTML" ); +}; + +/** + * Sets document-related variables once based on the current document + * @param {Element|Object} [doc] An element or document object to use to set the document + * @returns {Object} Returns the current document + */ +setDocument = Sizzle.setDocument = function( node ) { + var hasCompare, subWindow, + doc = node ? node.ownerDocument || node : preferredDoc; + + // Return early if doc is invalid or already selected + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( doc == document || doc.nodeType !== 9 || !doc.documentElement ) { + return document; + } + + // Update global variables + document = doc; + docElem = document.documentElement; + documentIsHTML = !isXML( document ); + + // Support: IE 9 - 11+, Edge 12 - 18+ + // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936) + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( preferredDoc != document && + ( subWindow = document.defaultView ) && subWindow.top !== subWindow ) { + + // Support: IE 11, Edge + if ( subWindow.addEventListener ) { + subWindow.addEventListener( "unload", unloadHandler, false ); + + // Support: IE 9 - 10 only + } else if ( subWindow.attachEvent ) { + subWindow.attachEvent( "onunload", unloadHandler ); + } + } + + // Support: IE 8 - 11+, Edge 12 - 18+, Chrome <=16 - 25 only, Firefox <=3.6 - 31 only, + // Safari 4 - 5 only, Opera <=11.6 - 12.x only + // IE/Edge & older browsers don't support the :scope pseudo-class. + // Support: Safari 6.0 only + // Safari 6.0 supports :scope but it's an alias of :root there. + support.scope = assert( function( el ) { + docElem.appendChild( el ).appendChild( document.createElement( "div" ) ); + return typeof el.querySelectorAll !== "undefined" && + !el.querySelectorAll( ":scope fieldset div" ).length; + } ); + + /* Attributes + ---------------------------------------------------------------------- */ + + // Support: IE<8 + // Verify that getAttribute really returns attributes and not properties + // (excepting IE8 booleans) + support.attributes = assert( function( el ) { + el.className = "i"; + return !el.getAttribute( "className" ); + } ); + + /* getElement(s)By* + ---------------------------------------------------------------------- */ + + // Check if getElementsByTagName("*") returns only elements + support.getElementsByTagName = assert( function( el ) { + el.appendChild( document.createComment( "" ) ); + return !el.getElementsByTagName( "*" ).length; + } ); + + // Support: IE<9 + support.getElementsByClassName = rnative.test( document.getElementsByClassName ); + + // Support: IE<10 + // Check if getElementById returns elements by name + // The broken getElementById methods don't pick up programmatically-set names, + // so use a roundabout getElementsByName test + support.getById = assert( function( el ) { + docElem.appendChild( el ).id = expando; + return !document.getElementsByName || !document.getElementsByName( expando ).length; + } ); + + // ID filter and find + if ( support.getById ) { + Expr.filter[ "ID" ] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + return elem.getAttribute( "id" ) === attrId; + }; + }; + Expr.find[ "ID" ] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var elem = context.getElementById( id ); + return elem ? [ elem ] : []; + } + }; + } else { + Expr.filter[ "ID" ] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + var node = typeof elem.getAttributeNode !== "undefined" && + elem.getAttributeNode( "id" ); + return node && node.value === attrId; + }; + }; + + // Support: IE 6 - 7 only + // getElementById is not reliable as a find shortcut + Expr.find[ "ID" ] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var node, i, elems, + elem = context.getElementById( id ); + + if ( elem ) { + + // Verify the id attribute + node = elem.getAttributeNode( "id" ); + if ( node && node.value === id ) { + return [ elem ]; + } + + // Fall back on getElementsByName + elems = context.getElementsByName( id ); + i = 0; + while ( ( elem = elems[ i++ ] ) ) { + node = elem.getAttributeNode( "id" ); + if ( node && node.value === id ) { + return [ elem ]; + } + } + } + + return []; + } + }; + } + + // Tag + Expr.find[ "TAG" ] = support.getElementsByTagName ? + function( tag, context ) { + if ( typeof context.getElementsByTagName !== "undefined" ) { + return context.getElementsByTagName( tag ); + + // DocumentFragment nodes don't have gEBTN + } else if ( support.qsa ) { + return context.querySelectorAll( tag ); + } + } : + + function( tag, context ) { + var elem, + tmp = [], + i = 0, + + // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too + results = context.getElementsByTagName( tag ); + + // Filter out possible comments + if ( tag === "*" ) { + while ( ( elem = results[ i++ ] ) ) { + if ( elem.nodeType === 1 ) { + tmp.push( elem ); + } + } + + return tmp; + } + return results; + }; + + // Class + Expr.find[ "CLASS" ] = support.getElementsByClassName && function( className, context ) { + if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) { + return context.getElementsByClassName( className ); + } + }; + + /* QSA/matchesSelector + ---------------------------------------------------------------------- */ + + // QSA and matchesSelector support + + // matchesSelector(:active) reports false when true (IE9/Opera 11.5) + rbuggyMatches = []; + + // qSa(:focus) reports false when true (Chrome 21) + // We allow this because of a bug in IE8/9 that throws an error + // whenever `document.activeElement` is accessed on an iframe + // So, we allow :focus to pass through QSA all the time to avoid the IE error + // See https://bugs.jquery.com/ticket/13378 + rbuggyQSA = []; + + if ( ( support.qsa = rnative.test( document.querySelectorAll ) ) ) { + + // Build QSA regex + // Regex strategy adopted from Diego Perini + assert( function( el ) { + + var input; + + // Select is set to empty string on purpose + // This is to test IE's treatment of not explicitly + // setting a boolean content attribute, + // since its presence should be enough + // https://bugs.jquery.com/ticket/12359 + docElem.appendChild( el ).innerHTML = "" + + ""; + + // Support: IE8, Opera 11-12.16 + // Nothing should be selected when empty strings follow ^= or $= or *= + // The test attribute must be unknown in Opera but "safe" for WinRT + // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section + if ( el.querySelectorAll( "[msallowcapture^='']" ).length ) { + rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); + } + + // Support: IE8 + // Boolean attributes and "value" are not treated correctly + if ( !el.querySelectorAll( "[selected]" ).length ) { + rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); + } + + // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+ + if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) { + rbuggyQSA.push( "~=" ); + } + + // Support: IE 11+, Edge 15 - 18+ + // IE 11/Edge don't find elements on a `[name='']` query in some cases. + // Adding a temporary attribute to the document before the selection works + // around the issue. + // Interestingly, IE 10 & older don't seem to have the issue. + input = document.createElement( "input" ); + input.setAttribute( "name", "" ); + el.appendChild( input ); + if ( !el.querySelectorAll( "[name='']" ).length ) { + rbuggyQSA.push( "\\[" + whitespace + "*name" + whitespace + "*=" + + whitespace + "*(?:''|\"\")" ); + } + + // Webkit/Opera - :checked should return selected option elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + // IE8 throws error here and will not see later tests + if ( !el.querySelectorAll( ":checked" ).length ) { + rbuggyQSA.push( ":checked" ); + } + + // Support: Safari 8+, iOS 8+ + // https://bugs.webkit.org/show_bug.cgi?id=136851 + // In-page `selector#id sibling-combinator selector` fails + if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) { + rbuggyQSA.push( ".#.+[+~]" ); + } + + // Support: Firefox <=3.6 - 5 only + // Old Firefox doesn't throw on a badly-escaped identifier. + el.querySelectorAll( "\\\f" ); + rbuggyQSA.push( "[\\r\\n\\f]" ); + } ); + + assert( function( el ) { + el.innerHTML = "" + + ""; + + // Support: Windows 8 Native Apps + // The type and name attributes are restricted during .innerHTML assignment + var input = document.createElement( "input" ); + input.setAttribute( "type", "hidden" ); + el.appendChild( input ).setAttribute( "name", "D" ); + + // Support: IE8 + // Enforce case-sensitivity of name attribute + if ( el.querySelectorAll( "[name=d]" ).length ) { + rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" ); + } + + // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled) + // IE8 throws error here and will not see later tests + if ( el.querySelectorAll( ":enabled" ).length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: IE9-11+ + // IE's :disabled selector does not pick up the children of disabled fieldsets + docElem.appendChild( el ).disabled = true; + if ( el.querySelectorAll( ":disabled" ).length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: Opera 10 - 11 only + // Opera 10-11 does not throw on post-comma invalid pseudos + el.querySelectorAll( "*,:x" ); + rbuggyQSA.push( ",.*:" ); + } ); + } + + if ( ( support.matchesSelector = rnative.test( ( matches = docElem.matches || + docElem.webkitMatchesSelector || + docElem.mozMatchesSelector || + docElem.oMatchesSelector || + docElem.msMatchesSelector ) ) ) ) { + + assert( function( el ) { + + // Check to see if it's possible to do matchesSelector + // on a disconnected node (IE 9) + support.disconnectedMatch = matches.call( el, "*" ); + + // This should fail with an exception + // Gecko does not error, returns false instead + matches.call( el, "[s!='']:x" ); + rbuggyMatches.push( "!=", pseudos ); + } ); + } + + rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join( "|" ) ); + rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join( "|" ) ); + + /* Contains + ---------------------------------------------------------------------- */ + hasCompare = rnative.test( docElem.compareDocumentPosition ); + + // Element contains another + // Purposefully self-exclusive + // As in, an element does not contain itself + contains = hasCompare || rnative.test( docElem.contains ) ? + function( a, b ) { + var adown = a.nodeType === 9 ? a.documentElement : a, + bup = b && b.parentNode; + return a === bup || !!( bup && bup.nodeType === 1 && ( + adown.contains ? + adown.contains( bup ) : + a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16 + ) ); + } : + function( a, b ) { + if ( b ) { + while ( ( b = b.parentNode ) ) { + if ( b === a ) { + return true; + } + } + } + return false; + }; + + /* Sorting + ---------------------------------------------------------------------- */ + + // Document order sorting + sortOrder = hasCompare ? + function( a, b ) { + + // Flag for duplicate removal + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + // Sort on method existence if only one input has compareDocumentPosition + var compare = !a.compareDocumentPosition - !b.compareDocumentPosition; + if ( compare ) { + return compare; + } + + // Calculate position if both inputs belong to the same document + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + compare = ( a.ownerDocument || a ) == ( b.ownerDocument || b ) ? + a.compareDocumentPosition( b ) : + + // Otherwise we know they are disconnected + 1; + + // Disconnected nodes + if ( compare & 1 || + ( !support.sortDetached && b.compareDocumentPosition( a ) === compare ) ) { + + // Choose the first element that is related to our preferred document + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( a == document || a.ownerDocument == preferredDoc && + contains( preferredDoc, a ) ) { + return -1; + } + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( b == document || b.ownerDocument == preferredDoc && + contains( preferredDoc, b ) ) { + return 1; + } + + // Maintain original order + return sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + } + + return compare & 4 ? -1 : 1; + } : + function( a, b ) { + + // Exit early if the nodes are identical + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + var cur, + i = 0, + aup = a.parentNode, + bup = b.parentNode, + ap = [ a ], + bp = [ b ]; + + // Parentless nodes are either documents or disconnected + if ( !aup || !bup ) { + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + /* eslint-disable eqeqeq */ + return a == document ? -1 : + b == document ? 1 : + /* eslint-enable eqeqeq */ + aup ? -1 : + bup ? 1 : + sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + + // If the nodes are siblings, we can do a quick check + } else if ( aup === bup ) { + return siblingCheck( a, b ); + } + + // Otherwise we need full lists of their ancestors for comparison + cur = a; + while ( ( cur = cur.parentNode ) ) { + ap.unshift( cur ); + } + cur = b; + while ( ( cur = cur.parentNode ) ) { + bp.unshift( cur ); + } + + // Walk down the tree looking for a discrepancy + while ( ap[ i ] === bp[ i ] ) { + i++; + } + + return i ? + + // Do a sibling check if the nodes have a common ancestor + siblingCheck( ap[ i ], bp[ i ] ) : + + // Otherwise nodes in our document sort first + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + /* eslint-disable eqeqeq */ + ap[ i ] == preferredDoc ? -1 : + bp[ i ] == preferredDoc ? 1 : + /* eslint-enable eqeqeq */ + 0; + }; + + return document; +}; + +Sizzle.matches = function( expr, elements ) { + return Sizzle( expr, null, null, elements ); +}; + +Sizzle.matchesSelector = function( elem, expr ) { + setDocument( elem ); + + if ( support.matchesSelector && documentIsHTML && + !nonnativeSelectorCache[ expr + " " ] && + ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) && + ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) { + + try { + var ret = matches.call( elem, expr ); + + // IE 9's matchesSelector returns false on disconnected nodes + if ( ret || support.disconnectedMatch || + + // As well, disconnected nodes are said to be in a document + // fragment in IE 9 + elem.document && elem.document.nodeType !== 11 ) { + return ret; + } + } catch ( e ) { + nonnativeSelectorCache( expr, true ); + } + } + + return Sizzle( expr, document, null, [ elem ] ).length > 0; +}; + +Sizzle.contains = function( context, elem ) { + + // Set document vars if needed + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( ( context.ownerDocument || context ) != document ) { + setDocument( context ); + } + return contains( context, elem ); +}; + +Sizzle.attr = function( elem, name ) { + + // Set document vars if needed + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( ( elem.ownerDocument || elem ) != document ) { + setDocument( elem ); + } + + var fn = Expr.attrHandle[ name.toLowerCase() ], + + // Don't get fooled by Object.prototype properties (jQuery #13807) + val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ? + fn( elem, name, !documentIsHTML ) : + undefined; + + return val !== undefined ? + val : + support.attributes || !documentIsHTML ? + elem.getAttribute( name ) : + ( val = elem.getAttributeNode( name ) ) && val.specified ? + val.value : + null; +}; + +Sizzle.escape = function( sel ) { + return ( sel + "" ).replace( rcssescape, fcssescape ); +}; + +Sizzle.error = function( msg ) { + throw new Error( "Syntax error, unrecognized expression: " + msg ); +}; + +/** + * Document sorting and removing duplicates + * @param {ArrayLike} results + */ +Sizzle.uniqueSort = function( results ) { + var elem, + duplicates = [], + j = 0, + i = 0; + + // Unless we *know* we can detect duplicates, assume their presence + hasDuplicate = !support.detectDuplicates; + sortInput = !support.sortStable && results.slice( 0 ); + results.sort( sortOrder ); + + if ( hasDuplicate ) { + while ( ( elem = results[ i++ ] ) ) { + if ( elem === results[ i ] ) { + j = duplicates.push( i ); + } + } + while ( j-- ) { + results.splice( duplicates[ j ], 1 ); + } + } + + // Clear input after sorting to release objects + // See https://github.com/jquery/sizzle/pull/225 + sortInput = null; + + return results; +}; + +/** + * Utility function for retrieving the text value of an array of DOM nodes + * @param {Array|Element} elem + */ +getText = Sizzle.getText = function( elem ) { + var node, + ret = "", + i = 0, + nodeType = elem.nodeType; + + if ( !nodeType ) { + + // If no nodeType, this is expected to be an array + while ( ( node = elem[ i++ ] ) ) { + + // Do not traverse comment nodes + ret += getText( node ); + } + } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { + + // Use textContent for elements + // innerText usage removed for consistency of new lines (jQuery #11153) + if ( typeof elem.textContent === "string" ) { + return elem.textContent; + } else { + + // Traverse its children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + ret += getText( elem ); + } + } + } else if ( nodeType === 3 || nodeType === 4 ) { + return elem.nodeValue; + } + + // Do not include comment or processing instruction nodes + + return ret; +}; + +Expr = Sizzle.selectors = { + + // Can be adjusted by the user + cacheLength: 50, + + createPseudo: markFunction, + + match: matchExpr, + + attrHandle: {}, + + find: {}, + + relative: { + ">": { dir: "parentNode", first: true }, + " ": { dir: "parentNode" }, + "+": { dir: "previousSibling", first: true }, + "~": { dir: "previousSibling" } + }, + + preFilter: { + "ATTR": function( match ) { + match[ 1 ] = match[ 1 ].replace( runescape, funescape ); + + // Move the given value to match[3] whether quoted or unquoted + match[ 3 ] = ( match[ 3 ] || match[ 4 ] || + match[ 5 ] || "" ).replace( runescape, funescape ); + + if ( match[ 2 ] === "~=" ) { + match[ 3 ] = " " + match[ 3 ] + " "; + } + + return match.slice( 0, 4 ); + }, + + "CHILD": function( match ) { + + /* matches from matchExpr["CHILD"] + 1 type (only|nth|...) + 2 what (child|of-type) + 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...) + 4 xn-component of xn+y argument ([+-]?\d*n|) + 5 sign of xn-component + 6 x of xn-component + 7 sign of y-component + 8 y of y-component + */ + match[ 1 ] = match[ 1 ].toLowerCase(); + + if ( match[ 1 ].slice( 0, 3 ) === "nth" ) { + + // nth-* requires argument + if ( !match[ 3 ] ) { + Sizzle.error( match[ 0 ] ); + } + + // numeric x and y parameters for Expr.filter.CHILD + // remember that false/true cast respectively to 0/1 + match[ 4 ] = +( match[ 4 ] ? + match[ 5 ] + ( match[ 6 ] || 1 ) : + 2 * ( match[ 3 ] === "even" || match[ 3 ] === "odd" ) ); + match[ 5 ] = +( ( match[ 7 ] + match[ 8 ] ) || match[ 3 ] === "odd" ); + + // other types prohibit arguments + } else if ( match[ 3 ] ) { + Sizzle.error( match[ 0 ] ); + } + + return match; + }, + + "PSEUDO": function( match ) { + var excess, + unquoted = !match[ 6 ] && match[ 2 ]; + + if ( matchExpr[ "CHILD" ].test( match[ 0 ] ) ) { + return null; + } + + // Accept quoted arguments as-is + if ( match[ 3 ] ) { + match[ 2 ] = match[ 4 ] || match[ 5 ] || ""; + + // Strip excess characters from unquoted arguments + } else if ( unquoted && rpseudo.test( unquoted ) && + + // Get excess from tokenize (recursively) + ( excess = tokenize( unquoted, true ) ) && + + // advance to the next closing parenthesis + ( excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length ) ) { + + // excess is a negative index + match[ 0 ] = match[ 0 ].slice( 0, excess ); + match[ 2 ] = unquoted.slice( 0, excess ); + } + + // Return only captures needed by the pseudo filter method (type and argument) + return match.slice( 0, 3 ); + } + }, + + filter: { + + "TAG": function( nodeNameSelector ) { + var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase(); + return nodeNameSelector === "*" ? + function() { + return true; + } : + function( elem ) { + return elem.nodeName && elem.nodeName.toLowerCase() === nodeName; + }; + }, + + "CLASS": function( className ) { + var pattern = classCache[ className + " " ]; + + return pattern || + ( pattern = new RegExp( "(^|" + whitespace + + ")" + className + "(" + whitespace + "|$)" ) ) && classCache( + className, function( elem ) { + return pattern.test( + typeof elem.className === "string" && elem.className || + typeof elem.getAttribute !== "undefined" && + elem.getAttribute( "class" ) || + "" + ); + } ); + }, + + "ATTR": function( name, operator, check ) { + return function( elem ) { + var result = Sizzle.attr( elem, name ); + + if ( result == null ) { + return operator === "!="; + } + if ( !operator ) { + return true; + } + + result += ""; + + /* eslint-disable max-len */ + + return operator === "=" ? result === check : + operator === "!=" ? result !== check : + operator === "^=" ? check && result.indexOf( check ) === 0 : + operator === "*=" ? check && result.indexOf( check ) > -1 : + operator === "$=" ? check && result.slice( -check.length ) === check : + operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 : + operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : + false; + /* eslint-enable max-len */ + + }; + }, + + "CHILD": function( type, what, _argument, first, last ) { + var simple = type.slice( 0, 3 ) !== "nth", + forward = type.slice( -4 ) !== "last", + ofType = what === "of-type"; + + return first === 1 && last === 0 ? + + // Shortcut for :nth-*(n) + function( elem ) { + return !!elem.parentNode; + } : + + function( elem, _context, xml ) { + var cache, uniqueCache, outerCache, node, nodeIndex, start, + dir = simple !== forward ? "nextSibling" : "previousSibling", + parent = elem.parentNode, + name = ofType && elem.nodeName.toLowerCase(), + useCache = !xml && !ofType, + diff = false; + + if ( parent ) { + + // :(first|last|only)-(child|of-type) + if ( simple ) { + while ( dir ) { + node = elem; + while ( ( node = node[ dir ] ) ) { + if ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) { + + return false; + } + } + + // Reverse direction for :only-* (if we haven't yet done so) + start = dir = type === "only" && !start && "nextSibling"; + } + return true; + } + + start = [ forward ? parent.firstChild : parent.lastChild ]; + + // non-xml :nth-child(...) stores cache data on `parent` + if ( forward && useCache ) { + + // Seek `elem` from a previously-cached index + + // ...in a gzip-friendly way + node = parent; + outerCache = node[ expando ] || ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex && cache[ 2 ]; + node = nodeIndex && parent.childNodes[ nodeIndex ]; + + while ( ( node = ++nodeIndex && node && node[ dir ] || + + // Fallback to seeking `elem` from the start + ( diff = nodeIndex = 0 ) || start.pop() ) ) { + + // When found, cache indexes on `parent` and break + if ( node.nodeType === 1 && ++diff && node === elem ) { + uniqueCache[ type ] = [ dirruns, nodeIndex, diff ]; + break; + } + } + + } else { + + // Use previously-cached element index if available + if ( useCache ) { + + // ...in a gzip-friendly way + node = elem; + outerCache = node[ expando ] || ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex; + } + + // xml :nth-child(...) + // or :nth-last-child(...) or :nth(-last)?-of-type(...) + if ( diff === false ) { + + // Use the same loop as above to seek `elem` from the start + while ( ( node = ++nodeIndex && node && node[ dir ] || + ( diff = nodeIndex = 0 ) || start.pop() ) ) { + + if ( ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) && + ++diff ) { + + // Cache the index of each encountered element + if ( useCache ) { + outerCache = node[ expando ] || + ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + uniqueCache[ type ] = [ dirruns, diff ]; + } + + if ( node === elem ) { + break; + } + } + } + } + } + + // Incorporate the offset, then check against cycle size + diff -= last; + return diff === first || ( diff % first === 0 && diff / first >= 0 ); + } + }; + }, + + "PSEUDO": function( pseudo, argument ) { + + // pseudo-class names are case-insensitive + // http://www.w3.org/TR/selectors/#pseudo-classes + // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters + // Remember that setFilters inherits from pseudos + var args, + fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] || + Sizzle.error( "unsupported pseudo: " + pseudo ); + + // The user may use createPseudo to indicate that + // arguments are needed to create the filter function + // just as Sizzle does + if ( fn[ expando ] ) { + return fn( argument ); + } + + // But maintain support for old signatures + if ( fn.length > 1 ) { + args = [ pseudo, pseudo, "", argument ]; + return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ? + markFunction( function( seed, matches ) { + var idx, + matched = fn( seed, argument ), + i = matched.length; + while ( i-- ) { + idx = indexOf( seed, matched[ i ] ); + seed[ idx ] = !( matches[ idx ] = matched[ i ] ); + } + } ) : + function( elem ) { + return fn( elem, 0, args ); + }; + } + + return fn; + } + }, + + pseudos: { + + // Potentially complex pseudos + "not": markFunction( function( selector ) { + + // Trim the selector passed to compile + // to avoid treating leading and trailing + // spaces as combinators + var input = [], + results = [], + matcher = compile( selector.replace( rtrim, "$1" ) ); + + return matcher[ expando ] ? + markFunction( function( seed, matches, _context, xml ) { + var elem, + unmatched = matcher( seed, null, xml, [] ), + i = seed.length; + + // Match elements unmatched by `matcher` + while ( i-- ) { + if ( ( elem = unmatched[ i ] ) ) { + seed[ i ] = !( matches[ i ] = elem ); + } + } + } ) : + function( elem, _context, xml ) { + input[ 0 ] = elem; + matcher( input, null, xml, results ); + + // Don't keep the element (issue #299) + input[ 0 ] = null; + return !results.pop(); + }; + } ), + + "has": markFunction( function( selector ) { + return function( elem ) { + return Sizzle( selector, elem ).length > 0; + }; + } ), + + "contains": markFunction( function( text ) { + text = text.replace( runescape, funescape ); + return function( elem ) { + return ( elem.textContent || getText( elem ) ).indexOf( text ) > -1; + }; + } ), + + // "Whether an element is represented by a :lang() selector + // is based solely on the element's language value + // being equal to the identifier C, + // or beginning with the identifier C immediately followed by "-". + // The matching of C against the element's language value is performed case-insensitively. + // The identifier C does not have to be a valid language name." + // http://www.w3.org/TR/selectors/#lang-pseudo + "lang": markFunction( function( lang ) { + + // lang value must be a valid identifier + if ( !ridentifier.test( lang || "" ) ) { + Sizzle.error( "unsupported lang: " + lang ); + } + lang = lang.replace( runescape, funescape ).toLowerCase(); + return function( elem ) { + var elemLang; + do { + if ( ( elemLang = documentIsHTML ? + elem.lang : + elem.getAttribute( "xml:lang" ) || elem.getAttribute( "lang" ) ) ) { + + elemLang = elemLang.toLowerCase(); + return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0; + } + } while ( ( elem = elem.parentNode ) && elem.nodeType === 1 ); + return false; + }; + } ), + + // Miscellaneous + "target": function( elem ) { + var hash = window.location && window.location.hash; + return hash && hash.slice( 1 ) === elem.id; + }, + + "root": function( elem ) { + return elem === docElem; + }, + + "focus": function( elem ) { + return elem === document.activeElement && + ( !document.hasFocus || document.hasFocus() ) && + !!( elem.type || elem.href || ~elem.tabIndex ); + }, + + // Boolean properties + "enabled": createDisabledPseudo( false ), + "disabled": createDisabledPseudo( true ), + + "checked": function( elem ) { + + // In CSS3, :checked should return both checked and selected elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + var nodeName = elem.nodeName.toLowerCase(); + return ( nodeName === "input" && !!elem.checked ) || + ( nodeName === "option" && !!elem.selected ); + }, + + "selected": function( elem ) { + + // Accessing this property makes selected-by-default + // options in Safari work properly + if ( elem.parentNode ) { + // eslint-disable-next-line no-unused-expressions + elem.parentNode.selectedIndex; + } + + return elem.selected === true; + }, + + // Contents + "empty": function( elem ) { + + // http://www.w3.org/TR/selectors/#empty-pseudo + // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5), + // but not by others (comment: 8; processing instruction: 7; etc.) + // nodeType < 6 works because attributes (2) do not appear as children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + if ( elem.nodeType < 6 ) { + return false; + } + } + return true; + }, + + "parent": function( elem ) { + return !Expr.pseudos[ "empty" ]( elem ); + }, + + // Element/input types + "header": function( elem ) { + return rheader.test( elem.nodeName ); + }, + + "input": function( elem ) { + return rinputs.test( elem.nodeName ); + }, + + "button": function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === "button" || name === "button"; + }, + + "text": function( elem ) { + var attr; + return elem.nodeName.toLowerCase() === "input" && + elem.type === "text" && + + // Support: IE<8 + // New HTML5 attribute values (e.g., "search") appear with elem.type === "text" + ( ( attr = elem.getAttribute( "type" ) ) == null || + attr.toLowerCase() === "text" ); + }, + + // Position-in-collection + "first": createPositionalPseudo( function() { + return [ 0 ]; + } ), + + "last": createPositionalPseudo( function( _matchIndexes, length ) { + return [ length - 1 ]; + } ), + + "eq": createPositionalPseudo( function( _matchIndexes, length, argument ) { + return [ argument < 0 ? argument + length : argument ]; + } ), + + "even": createPositionalPseudo( function( matchIndexes, length ) { + var i = 0; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "odd": createPositionalPseudo( function( matchIndexes, length ) { + var i = 1; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "lt": createPositionalPseudo( function( matchIndexes, length, argument ) { + var i = argument < 0 ? + argument + length : + argument > length ? + length : + argument; + for ( ; --i >= 0; ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "gt": createPositionalPseudo( function( matchIndexes, length, argument ) { + var i = argument < 0 ? argument + length : argument; + for ( ; ++i < length; ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ) + } +}; + +Expr.pseudos[ "nth" ] = Expr.pseudos[ "eq" ]; + +// Add button/input type pseudos +for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) { + Expr.pseudos[ i ] = createInputPseudo( i ); +} +for ( i in { submit: true, reset: true } ) { + Expr.pseudos[ i ] = createButtonPseudo( i ); +} + +// Easy API for creating new setFilters +function setFilters() {} +setFilters.prototype = Expr.filters = Expr.pseudos; +Expr.setFilters = new setFilters(); + +tokenize = Sizzle.tokenize = function( selector, parseOnly ) { + var matched, match, tokens, type, + soFar, groups, preFilters, + cached = tokenCache[ selector + " " ]; + + if ( cached ) { + return parseOnly ? 0 : cached.slice( 0 ); + } + + soFar = selector; + groups = []; + preFilters = Expr.preFilter; + + while ( soFar ) { + + // Comma and first run + if ( !matched || ( match = rcomma.exec( soFar ) ) ) { + if ( match ) { + + // Don't consume trailing commas as valid + soFar = soFar.slice( match[ 0 ].length ) || soFar; + } + groups.push( ( tokens = [] ) ); + } + + matched = false; + + // Combinators + if ( ( match = rcombinators.exec( soFar ) ) ) { + matched = match.shift(); + tokens.push( { + value: matched, + + // Cast descendant combinators to space + type: match[ 0 ].replace( rtrim, " " ) + } ); + soFar = soFar.slice( matched.length ); + } + + // Filters + for ( type in Expr.filter ) { + if ( ( match = matchExpr[ type ].exec( soFar ) ) && ( !preFilters[ type ] || + ( match = preFilters[ type ]( match ) ) ) ) { + matched = match.shift(); + tokens.push( { + value: matched, + type: type, + matches: match + } ); + soFar = soFar.slice( matched.length ); + } + } + + if ( !matched ) { + break; + } + } + + // Return the length of the invalid excess + // if we're just parsing + // Otherwise, throw an error or return tokens + return parseOnly ? + soFar.length : + soFar ? + Sizzle.error( selector ) : + + // Cache the tokens + tokenCache( selector, groups ).slice( 0 ); +}; + +function toSelector( tokens ) { + var i = 0, + len = tokens.length, + selector = ""; + for ( ; i < len; i++ ) { + selector += tokens[ i ].value; + } + return selector; +} + +function addCombinator( matcher, combinator, base ) { + var dir = combinator.dir, + skip = combinator.next, + key = skip || dir, + checkNonElements = base && key === "parentNode", + doneName = done++; + + return combinator.first ? + + // Check against closest ancestor/preceding element + function( elem, context, xml ) { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + return matcher( elem, context, xml ); + } + } + return false; + } : + + // Check against all ancestor/preceding elements + function( elem, context, xml ) { + var oldCache, uniqueCache, outerCache, + newCache = [ dirruns, doneName ]; + + // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching + if ( xml ) { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + if ( matcher( elem, context, xml ) ) { + return true; + } + } + } + } else { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + outerCache = elem[ expando ] || ( elem[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ elem.uniqueID ] || + ( outerCache[ elem.uniqueID ] = {} ); + + if ( skip && skip === elem.nodeName.toLowerCase() ) { + elem = elem[ dir ] || elem; + } else if ( ( oldCache = uniqueCache[ key ] ) && + oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) { + + // Assign to newCache so results back-propagate to previous elements + return ( newCache[ 2 ] = oldCache[ 2 ] ); + } else { + + // Reuse newcache so results back-propagate to previous elements + uniqueCache[ key ] = newCache; + + // A match means we're done; a fail means we have to keep checking + if ( ( newCache[ 2 ] = matcher( elem, context, xml ) ) ) { + return true; + } + } + } + } + } + return false; + }; +} + +function elementMatcher( matchers ) { + return matchers.length > 1 ? + function( elem, context, xml ) { + var i = matchers.length; + while ( i-- ) { + if ( !matchers[ i ]( elem, context, xml ) ) { + return false; + } + } + return true; + } : + matchers[ 0 ]; +} + +function multipleContexts( selector, contexts, results ) { + var i = 0, + len = contexts.length; + for ( ; i < len; i++ ) { + Sizzle( selector, contexts[ i ], results ); + } + return results; +} + +function condense( unmatched, map, filter, context, xml ) { + var elem, + newUnmatched = [], + i = 0, + len = unmatched.length, + mapped = map != null; + + for ( ; i < len; i++ ) { + if ( ( elem = unmatched[ i ] ) ) { + if ( !filter || filter( elem, context, xml ) ) { + newUnmatched.push( elem ); + if ( mapped ) { + map.push( i ); + } + } + } + } + + return newUnmatched; +} + +function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) { + if ( postFilter && !postFilter[ expando ] ) { + postFilter = setMatcher( postFilter ); + } + if ( postFinder && !postFinder[ expando ] ) { + postFinder = setMatcher( postFinder, postSelector ); + } + return markFunction( function( seed, results, context, xml ) { + var temp, i, elem, + preMap = [], + postMap = [], + preexisting = results.length, + + // Get initial elements from seed or context + elems = seed || multipleContexts( + selector || "*", + context.nodeType ? [ context ] : context, + [] + ), + + // Prefilter to get matcher input, preserving a map for seed-results synchronization + matcherIn = preFilter && ( seed || !selector ) ? + condense( elems, preMap, preFilter, context, xml ) : + elems, + + matcherOut = matcher ? + + // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results, + postFinder || ( seed ? preFilter : preexisting || postFilter ) ? + + // ...intermediate processing is necessary + [] : + + // ...otherwise use results directly + results : + matcherIn; + + // Find primary matches + if ( matcher ) { + matcher( matcherIn, matcherOut, context, xml ); + } + + // Apply postFilter + if ( postFilter ) { + temp = condense( matcherOut, postMap ); + postFilter( temp, [], context, xml ); + + // Un-match failing elements by moving them back to matcherIn + i = temp.length; + while ( i-- ) { + if ( ( elem = temp[ i ] ) ) { + matcherOut[ postMap[ i ] ] = !( matcherIn[ postMap[ i ] ] = elem ); + } + } + } + + if ( seed ) { + if ( postFinder || preFilter ) { + if ( postFinder ) { + + // Get the final matcherOut by condensing this intermediate into postFinder contexts + temp = []; + i = matcherOut.length; + while ( i-- ) { + if ( ( elem = matcherOut[ i ] ) ) { + + // Restore matcherIn since elem is not yet a final match + temp.push( ( matcherIn[ i ] = elem ) ); + } + } + postFinder( null, ( matcherOut = [] ), temp, xml ); + } + + // Move matched elements from seed to results to keep them synchronized + i = matcherOut.length; + while ( i-- ) { + if ( ( elem = matcherOut[ i ] ) && + ( temp = postFinder ? indexOf( seed, elem ) : preMap[ i ] ) > -1 ) { + + seed[ temp ] = !( results[ temp ] = elem ); + } + } + } + + // Add elements to results, through postFinder if defined + } else { + matcherOut = condense( + matcherOut === results ? + matcherOut.splice( preexisting, matcherOut.length ) : + matcherOut + ); + if ( postFinder ) { + postFinder( null, results, matcherOut, xml ); + } else { + push.apply( results, matcherOut ); + } + } + } ); +} + +function matcherFromTokens( tokens ) { + var checkContext, matcher, j, + len = tokens.length, + leadingRelative = Expr.relative[ tokens[ 0 ].type ], + implicitRelative = leadingRelative || Expr.relative[ " " ], + i = leadingRelative ? 1 : 0, + + // The foundational matcher ensures that elements are reachable from top-level context(s) + matchContext = addCombinator( function( elem ) { + return elem === checkContext; + }, implicitRelative, true ), + matchAnyContext = addCombinator( function( elem ) { + return indexOf( checkContext, elem ) > -1; + }, implicitRelative, true ), + matchers = [ function( elem, context, xml ) { + var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( + ( checkContext = context ).nodeType ? + matchContext( elem, context, xml ) : + matchAnyContext( elem, context, xml ) ); + + // Avoid hanging onto element (issue #299) + checkContext = null; + return ret; + } ]; + + for ( ; i < len; i++ ) { + if ( ( matcher = Expr.relative[ tokens[ i ].type ] ) ) { + matchers = [ addCombinator( elementMatcher( matchers ), matcher ) ]; + } else { + matcher = Expr.filter[ tokens[ i ].type ].apply( null, tokens[ i ].matches ); + + // Return special upon seeing a positional matcher + if ( matcher[ expando ] ) { + + // Find the next relative operator (if any) for proper handling + j = ++i; + for ( ; j < len; j++ ) { + if ( Expr.relative[ tokens[ j ].type ] ) { + break; + } + } + return setMatcher( + i > 1 && elementMatcher( matchers ), + i > 1 && toSelector( + + // If the preceding token was a descendant combinator, insert an implicit any-element `*` + tokens + .slice( 0, i - 1 ) + .concat( { value: tokens[ i - 2 ].type === " " ? "*" : "" } ) + ).replace( rtrim, "$1" ), + matcher, + i < j && matcherFromTokens( tokens.slice( i, j ) ), + j < len && matcherFromTokens( ( tokens = tokens.slice( j ) ) ), + j < len && toSelector( tokens ) + ); + } + matchers.push( matcher ); + } + } + + return elementMatcher( matchers ); +} + +function matcherFromGroupMatchers( elementMatchers, setMatchers ) { + var bySet = setMatchers.length > 0, + byElement = elementMatchers.length > 0, + superMatcher = function( seed, context, xml, results, outermost ) { + var elem, j, matcher, + matchedCount = 0, + i = "0", + unmatched = seed && [], + setMatched = [], + contextBackup = outermostContext, + + // We must always have either seed elements or outermost context + elems = seed || byElement && Expr.find[ "TAG" ]( "*", outermost ), + + // Use integer dirruns iff this is the outermost matcher + dirrunsUnique = ( dirruns += contextBackup == null ? 1 : Math.random() || 0.1 ), + len = elems.length; + + if ( outermost ) { + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + outermostContext = context == document || context || outermost; + } + + // Add elements passing elementMatchers directly to results + // Support: IE<9, Safari + // Tolerate NodeList properties (IE: "length"; Safari: ) matching elements by id + for ( ; i !== len && ( elem = elems[ i ] ) != null; i++ ) { + if ( byElement && elem ) { + j = 0; + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( !context && elem.ownerDocument != document ) { + setDocument( elem ); + xml = !documentIsHTML; + } + while ( ( matcher = elementMatchers[ j++ ] ) ) { + if ( matcher( elem, context || document, xml ) ) { + results.push( elem ); + break; + } + } + if ( outermost ) { + dirruns = dirrunsUnique; + } + } + + // Track unmatched elements for set filters + if ( bySet ) { + + // They will have gone through all possible matchers + if ( ( elem = !matcher && elem ) ) { + matchedCount--; + } + + // Lengthen the array for every element, matched or not + if ( seed ) { + unmatched.push( elem ); + } + } + } + + // `i` is now the count of elements visited above, and adding it to `matchedCount` + // makes the latter nonnegative. + matchedCount += i; + + // Apply set filters to unmatched elements + // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount` + // equals `i`), unless we didn't visit _any_ elements in the above loop because we have + // no element matchers and no seed. + // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that + // case, which will result in a "00" `matchedCount` that differs from `i` but is also + // numerically zero. + if ( bySet && i !== matchedCount ) { + j = 0; + while ( ( matcher = setMatchers[ j++ ] ) ) { + matcher( unmatched, setMatched, context, xml ); + } + + if ( seed ) { + + // Reintegrate element matches to eliminate the need for sorting + if ( matchedCount > 0 ) { + while ( i-- ) { + if ( !( unmatched[ i ] || setMatched[ i ] ) ) { + setMatched[ i ] = pop.call( results ); + } + } + } + + // Discard index placeholder values to get only actual matches + setMatched = condense( setMatched ); + } + + // Add matches to results + push.apply( results, setMatched ); + + // Seedless set matches succeeding multiple successful matchers stipulate sorting + if ( outermost && !seed && setMatched.length > 0 && + ( matchedCount + setMatchers.length ) > 1 ) { + + Sizzle.uniqueSort( results ); + } + } + + // Override manipulation of globals by nested matchers + if ( outermost ) { + dirruns = dirrunsUnique; + outermostContext = contextBackup; + } + + return unmatched; + }; + + return bySet ? + markFunction( superMatcher ) : + superMatcher; +} + +compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) { + var i, + setMatchers = [], + elementMatchers = [], + cached = compilerCache[ selector + " " ]; + + if ( !cached ) { + + // Generate a function of recursive functions that can be used to check each element + if ( !match ) { + match = tokenize( selector ); + } + i = match.length; + while ( i-- ) { + cached = matcherFromTokens( match[ i ] ); + if ( cached[ expando ] ) { + setMatchers.push( cached ); + } else { + elementMatchers.push( cached ); + } + } + + // Cache the compiled function + cached = compilerCache( + selector, + matcherFromGroupMatchers( elementMatchers, setMatchers ) + ); + + // Save selector and tokenization + cached.selector = selector; + } + return cached; +}; + +/** + * A low-level selection function that works with Sizzle's compiled + * selector functions + * @param {String|Function} selector A selector or a pre-compiled + * selector function built with Sizzle.compile + * @param {Element} context + * @param {Array} [results] + * @param {Array} [seed] A set of elements to match against + */ +select = Sizzle.select = function( selector, context, results, seed ) { + var i, tokens, token, type, find, + compiled = typeof selector === "function" && selector, + match = !seed && tokenize( ( selector = compiled.selector || selector ) ); + + results = results || []; + + // Try to minimize operations if there is only one selector in the list and no seed + // (the latter of which guarantees us context) + if ( match.length === 1 ) { + + // Reduce context if the leading compound selector is an ID + tokens = match[ 0 ] = match[ 0 ].slice( 0 ); + if ( tokens.length > 2 && ( token = tokens[ 0 ] ).type === "ID" && + context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[ 1 ].type ] ) { + + context = ( Expr.find[ "ID" ]( token.matches[ 0 ] + .replace( runescape, funescape ), context ) || [] )[ 0 ]; + if ( !context ) { + return results; + + // Precompiled matchers will still verify ancestry, so step up a level + } else if ( compiled ) { + context = context.parentNode; + } + + selector = selector.slice( tokens.shift().value.length ); + } + + // Fetch a seed set for right-to-left matching + i = matchExpr[ "needsContext" ].test( selector ) ? 0 : tokens.length; + while ( i-- ) { + token = tokens[ i ]; + + // Abort if we hit a combinator + if ( Expr.relative[ ( type = token.type ) ] ) { + break; + } + if ( ( find = Expr.find[ type ] ) ) { + + // Search, expanding context for leading sibling combinators + if ( ( seed = find( + token.matches[ 0 ].replace( runescape, funescape ), + rsibling.test( tokens[ 0 ].type ) && testContext( context.parentNode ) || + context + ) ) ) { + + // If seed is empty or no tokens remain, we can return early + tokens.splice( i, 1 ); + selector = seed.length && toSelector( tokens ); + if ( !selector ) { + push.apply( results, seed ); + return results; + } + + break; + } + } + } + } + + // Compile and execute a filtering function if one is not provided + // Provide `match` to avoid retokenization if we modified the selector above + ( compiled || compile( selector, match ) )( + seed, + context, + !documentIsHTML, + results, + !context || rsibling.test( selector ) && testContext( context.parentNode ) || context + ); + return results; +}; + +// One-time assignments + +// Sort stability +support.sortStable = expando.split( "" ).sort( sortOrder ).join( "" ) === expando; + +// Support: Chrome 14-35+ +// Always assume duplicates if they aren't passed to the comparison function +support.detectDuplicates = !!hasDuplicate; + +// Initialize against the default document +setDocument(); + +// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27) +// Detached nodes confoundingly follow *each other* +support.sortDetached = assert( function( el ) { + + // Should return 1, but returns 4 (following) + return el.compareDocumentPosition( document.createElement( "fieldset" ) ) & 1; +} ); + +// Support: IE<8 +// Prevent attribute/property "interpolation" +// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx +if ( !assert( function( el ) { + el.innerHTML = ""; + return el.firstChild.getAttribute( "href" ) === "#"; +} ) ) { + addHandle( "type|href|height|width", function( elem, name, isXML ) { + if ( !isXML ) { + return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 ); + } + } ); +} + +// Support: IE<9 +// Use defaultValue in place of getAttribute("value") +if ( !support.attributes || !assert( function( el ) { + el.innerHTML = ""; + el.firstChild.setAttribute( "value", "" ); + return el.firstChild.getAttribute( "value" ) === ""; +} ) ) { + addHandle( "value", function( elem, _name, isXML ) { + if ( !isXML && elem.nodeName.toLowerCase() === "input" ) { + return elem.defaultValue; + } + } ); +} + +// Support: IE<9 +// Use getAttributeNode to fetch booleans when getAttribute lies +if ( !assert( function( el ) { + return el.getAttribute( "disabled" ) == null; +} ) ) { + addHandle( booleans, function( elem, name, isXML ) { + var val; + if ( !isXML ) { + return elem[ name ] === true ? name.toLowerCase() : + ( val = elem.getAttributeNode( name ) ) && val.specified ? + val.value : + null; + } + } ); +} + +return Sizzle; + +} )( window ); + + + +jQuery.find = Sizzle; +jQuery.expr = Sizzle.selectors; + +// Deprecated +jQuery.expr[ ":" ] = jQuery.expr.pseudos; +jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort; +jQuery.text = Sizzle.getText; +jQuery.isXMLDoc = Sizzle.isXML; +jQuery.contains = Sizzle.contains; +jQuery.escapeSelector = Sizzle.escape; + + + + +var dir = function( elem, dir, until ) { + var matched = [], + truncate = until !== undefined; + + while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) { + if ( elem.nodeType === 1 ) { + if ( truncate && jQuery( elem ).is( until ) ) { + break; + } + matched.push( elem ); + } + } + return matched; +}; + + +var siblings = function( n, elem ) { + var matched = []; + + for ( ; n; n = n.nextSibling ) { + if ( n.nodeType === 1 && n !== elem ) { + matched.push( n ); + } + } + + return matched; +}; + + +var rneedsContext = jQuery.expr.match.needsContext; + + + +function nodeName( elem, name ) { + + return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); + +}; +var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i ); + + + +// Implement the identical functionality for filter and not +function winnow( elements, qualifier, not ) { + if ( isFunction( qualifier ) ) { + return jQuery.grep( elements, function( elem, i ) { + return !!qualifier.call( elem, i, elem ) !== not; + } ); + } + + // Single element + if ( qualifier.nodeType ) { + return jQuery.grep( elements, function( elem ) { + return ( elem === qualifier ) !== not; + } ); + } + + // Arraylike of elements (jQuery, arguments, Array) + if ( typeof qualifier !== "string" ) { + return jQuery.grep( elements, function( elem ) { + return ( indexOf.call( qualifier, elem ) > -1 ) !== not; + } ); + } + + // Filtered directly for both simple and complex selectors + return jQuery.filter( qualifier, elements, not ); +} + +jQuery.filter = function( expr, elems, not ) { + var elem = elems[ 0 ]; + + if ( not ) { + expr = ":not(" + expr + ")"; + } + + if ( elems.length === 1 && elem.nodeType === 1 ) { + return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : []; + } + + return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) { + return elem.nodeType === 1; + } ) ); +}; + +jQuery.fn.extend( { + find: function( selector ) { + var i, ret, + len = this.length, + self = this; + + if ( typeof selector !== "string" ) { + return this.pushStack( jQuery( selector ).filter( function() { + for ( i = 0; i < len; i++ ) { + if ( jQuery.contains( self[ i ], this ) ) { + return true; + } + } + } ) ); + } + + ret = this.pushStack( [] ); + + for ( i = 0; i < len; i++ ) { + jQuery.find( selector, self[ i ], ret ); + } + + return len > 1 ? jQuery.uniqueSort( ret ) : ret; + }, + filter: function( selector ) { + return this.pushStack( winnow( this, selector || [], false ) ); + }, + not: function( selector ) { + return this.pushStack( winnow( this, selector || [], true ) ); + }, + is: function( selector ) { + return !!winnow( + this, + + // If this is a positional/relative selector, check membership in the returned set + // so $("p:first").is("p:last") won't return true for a doc with two "p". + typeof selector === "string" && rneedsContext.test( selector ) ? + jQuery( selector ) : + selector || [], + false + ).length; + } +} ); + + +// Initialize a jQuery object + + +// A central reference to the root jQuery(document) +var rootjQuery, + + // A simple way to check for HTML strings + // Prioritize #id over to avoid XSS via location.hash (#9521) + // Strict HTML recognition (#11290: must start with <) + // Shortcut simple #id case for speed + rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/, + + init = jQuery.fn.init = function( selector, context, root ) { + var match, elem; + + // HANDLE: $(""), $(null), $(undefined), $(false) + if ( !selector ) { + return this; + } + + // Method init() accepts an alternate rootjQuery + // so migrate can support jQuery.sub (gh-2101) + root = root || rootjQuery; + + // Handle HTML strings + if ( typeof selector === "string" ) { + if ( selector[ 0 ] === "<" && + selector[ selector.length - 1 ] === ">" && + selector.length >= 3 ) { + + // Assume that strings that start and end with <> are HTML and skip the regex check + match = [ null, selector, null ]; + + } else { + match = rquickExpr.exec( selector ); + } + + // Match html or make sure no context is specified for #id + if ( match && ( match[ 1 ] || !context ) ) { + + // HANDLE: $(html) -> $(array) + if ( match[ 1 ] ) { + context = context instanceof jQuery ? context[ 0 ] : context; + + // Option to run scripts is true for back-compat + // Intentionally let the error be thrown if parseHTML is not present + jQuery.merge( this, jQuery.parseHTML( + match[ 1 ], + context && context.nodeType ? context.ownerDocument || context : document, + true + ) ); + + // HANDLE: $(html, props) + if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) { + for ( match in context ) { + + // Properties of context are called as methods if possible + if ( isFunction( this[ match ] ) ) { + this[ match ]( context[ match ] ); + + // ...and otherwise set as attributes + } else { + this.attr( match, context[ match ] ); + } + } + } + + return this; + + // HANDLE: $(#id) + } else { + elem = document.getElementById( match[ 2 ] ); + + if ( elem ) { + + // Inject the element directly into the jQuery object + this[ 0 ] = elem; + this.length = 1; + } + return this; + } + + // HANDLE: $(expr, $(...)) + } else if ( !context || context.jquery ) { + return ( context || root ).find( selector ); + + // HANDLE: $(expr, context) + // (which is just equivalent to: $(context).find(expr) + } else { + return this.constructor( context ).find( selector ); + } + + // HANDLE: $(DOMElement) + } else if ( selector.nodeType ) { + this[ 0 ] = selector; + this.length = 1; + return this; + + // HANDLE: $(function) + // Shortcut for document ready + } else if ( isFunction( selector ) ) { + return root.ready !== undefined ? + root.ready( selector ) : + + // Execute immediately if ready is not present + selector( jQuery ); + } + + return jQuery.makeArray( selector, this ); + }; + +// Give the init function the jQuery prototype for later instantiation +init.prototype = jQuery.fn; + +// Initialize central reference +rootjQuery = jQuery( document ); + + +var rparentsprev = /^(?:parents|prev(?:Until|All))/, + + // Methods guaranteed to produce a unique set when starting from a unique set + guaranteedUnique = { + children: true, + contents: true, + next: true, + prev: true + }; + +jQuery.fn.extend( { + has: function( target ) { + var targets = jQuery( target, this ), + l = targets.length; + + return this.filter( function() { + var i = 0; + for ( ; i < l; i++ ) { + if ( jQuery.contains( this, targets[ i ] ) ) { + return true; + } + } + } ); + }, + + closest: function( selectors, context ) { + var cur, + i = 0, + l = this.length, + matched = [], + targets = typeof selectors !== "string" && jQuery( selectors ); + + // Positional selectors never match, since there's no _selection_ context + if ( !rneedsContext.test( selectors ) ) { + for ( ; i < l; i++ ) { + for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) { + + // Always skip document fragments + if ( cur.nodeType < 11 && ( targets ? + targets.index( cur ) > -1 : + + // Don't pass non-elements to Sizzle + cur.nodeType === 1 && + jQuery.find.matchesSelector( cur, selectors ) ) ) { + + matched.push( cur ); + break; + } + } + } + } + + return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched ); + }, + + // Determine the position of an element within the set + index: function( elem ) { + + // No argument, return index in parent + if ( !elem ) { + return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1; + } + + // Index in selector + if ( typeof elem === "string" ) { + return indexOf.call( jQuery( elem ), this[ 0 ] ); + } + + // Locate the position of the desired element + return indexOf.call( this, + + // If it receives a jQuery object, the first element is used + elem.jquery ? elem[ 0 ] : elem + ); + }, + + add: function( selector, context ) { + return this.pushStack( + jQuery.uniqueSort( + jQuery.merge( this.get(), jQuery( selector, context ) ) + ) + ); + }, + + addBack: function( selector ) { + return this.add( selector == null ? + this.prevObject : this.prevObject.filter( selector ) + ); + } +} ); + +function sibling( cur, dir ) { + while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {} + return cur; +} + +jQuery.each( { + parent: function( elem ) { + var parent = elem.parentNode; + return parent && parent.nodeType !== 11 ? parent : null; + }, + parents: function( elem ) { + return dir( elem, "parentNode" ); + }, + parentsUntil: function( elem, _i, until ) { + return dir( elem, "parentNode", until ); + }, + next: function( elem ) { + return sibling( elem, "nextSibling" ); + }, + prev: function( elem ) { + return sibling( elem, "previousSibling" ); + }, + nextAll: function( elem ) { + return dir( elem, "nextSibling" ); + }, + prevAll: function( elem ) { + return dir( elem, "previousSibling" ); + }, + nextUntil: function( elem, _i, until ) { + return dir( elem, "nextSibling", until ); + }, + prevUntil: function( elem, _i, until ) { + return dir( elem, "previousSibling", until ); + }, + siblings: function( elem ) { + return siblings( ( elem.parentNode || {} ).firstChild, elem ); + }, + children: function( elem ) { + return siblings( elem.firstChild ); + }, + contents: function( elem ) { + if ( elem.contentDocument != null && + + // Support: IE 11+ + // elements with no `data` attribute has an object + // `contentDocument` with a `null` prototype. + getProto( elem.contentDocument ) ) { + + return elem.contentDocument; + } + + // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only + // Treat the template element as a regular one in browsers that + // don't support it. + if ( nodeName( elem, "template" ) ) { + elem = elem.content || elem; + } + + return jQuery.merge( [], elem.childNodes ); + } +}, function( name, fn ) { + jQuery.fn[ name ] = function( until, selector ) { + var matched = jQuery.map( this, fn, until ); + + if ( name.slice( -5 ) !== "Until" ) { + selector = until; + } + + if ( selector && typeof selector === "string" ) { + matched = jQuery.filter( selector, matched ); + } + + if ( this.length > 1 ) { + + // Remove duplicates + if ( !guaranteedUnique[ name ] ) { + jQuery.uniqueSort( matched ); + } + + // Reverse order for parents* and prev-derivatives + if ( rparentsprev.test( name ) ) { + matched.reverse(); + } + } + + return this.pushStack( matched ); + }; +} ); +var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g ); + + + +// Convert String-formatted options into Object-formatted ones +function createOptions( options ) { + var object = {}; + jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) { + object[ flag ] = true; + } ); + return object; +} + +/* + * Create a callback list using the following parameters: + * + * options: an optional list of space-separated options that will change how + * the callback list behaves or a more traditional option object + * + * By default a callback list will act like an event callback list and can be + * "fired" multiple times. + * + * Possible options: + * + * once: will ensure the callback list can only be fired once (like a Deferred) + * + * memory: will keep track of previous values and will call any callback added + * after the list has been fired right away with the latest "memorized" + * values (like a Deferred) + * + * unique: will ensure a callback can only be added once (no duplicate in the list) + * + * stopOnFalse: interrupt callings when a callback returns false + * + */ +jQuery.Callbacks = function( options ) { + + // Convert options from String-formatted to Object-formatted if needed + // (we check in cache first) + options = typeof options === "string" ? + createOptions( options ) : + jQuery.extend( {}, options ); + + var // Flag to know if list is currently firing + firing, + + // Last fire value for non-forgettable lists + memory, + + // Flag to know if list was already fired + fired, + + // Flag to prevent firing + locked, + + // Actual callback list + list = [], + + // Queue of execution data for repeatable lists + queue = [], + + // Index of currently firing callback (modified by add/remove as needed) + firingIndex = -1, + + // Fire callbacks + fire = function() { + + // Enforce single-firing + locked = locked || options.once; + + // Execute callbacks for all pending executions, + // respecting firingIndex overrides and runtime changes + fired = firing = true; + for ( ; queue.length; firingIndex = -1 ) { + memory = queue.shift(); + while ( ++firingIndex < list.length ) { + + // Run callback and check for early termination + if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false && + options.stopOnFalse ) { + + // Jump to end and forget the data so .add doesn't re-fire + firingIndex = list.length; + memory = false; + } + } + } + + // Forget the data if we're done with it + if ( !options.memory ) { + memory = false; + } + + firing = false; + + // Clean up if we're done firing for good + if ( locked ) { + + // Keep an empty list if we have data for future add calls + if ( memory ) { + list = []; + + // Otherwise, this object is spent + } else { + list = ""; + } + } + }, + + // Actual Callbacks object + self = { + + // Add a callback or a collection of callbacks to the list + add: function() { + if ( list ) { + + // If we have memory from a past run, we should fire after adding + if ( memory && !firing ) { + firingIndex = list.length - 1; + queue.push( memory ); + } + + ( function add( args ) { + jQuery.each( args, function( _, arg ) { + if ( isFunction( arg ) ) { + if ( !options.unique || !self.has( arg ) ) { + list.push( arg ); + } + } else if ( arg && arg.length && toType( arg ) !== "string" ) { + + // Inspect recursively + add( arg ); + } + } ); + } )( arguments ); + + if ( memory && !firing ) { + fire(); + } + } + return this; + }, + + // Remove a callback from the list + remove: function() { + jQuery.each( arguments, function( _, arg ) { + var index; + while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) { + list.splice( index, 1 ); + + // Handle firing indexes + if ( index <= firingIndex ) { + firingIndex--; + } + } + } ); + return this; + }, + + // Check if a given callback is in the list. + // If no argument is given, return whether or not list has callbacks attached. + has: function( fn ) { + return fn ? + jQuery.inArray( fn, list ) > -1 : + list.length > 0; + }, + + // Remove all callbacks from the list + empty: function() { + if ( list ) { + list = []; + } + return this; + }, + + // Disable .fire and .add + // Abort any current/pending executions + // Clear all callbacks and values + disable: function() { + locked = queue = []; + list = memory = ""; + return this; + }, + disabled: function() { + return !list; + }, + + // Disable .fire + // Also disable .add unless we have memory (since it would have no effect) + // Abort any pending executions + lock: function() { + locked = queue = []; + if ( !memory && !firing ) { + list = memory = ""; + } + return this; + }, + locked: function() { + return !!locked; + }, + + // Call all callbacks with the given context and arguments + fireWith: function( context, args ) { + if ( !locked ) { + args = args || []; + args = [ context, args.slice ? args.slice() : args ]; + queue.push( args ); + if ( !firing ) { + fire(); + } + } + return this; + }, + + // Call all the callbacks with the given arguments + fire: function() { + self.fireWith( this, arguments ); + return this; + }, + + // To know if the callbacks have already been called at least once + fired: function() { + return !!fired; + } + }; + + return self; +}; + + +function Identity( v ) { + return v; +} +function Thrower( ex ) { + throw ex; +} + +function adoptValue( value, resolve, reject, noValue ) { + var method; + + try { + + // Check for promise aspect first to privilege synchronous behavior + if ( value && isFunction( ( method = value.promise ) ) ) { + method.call( value ).done( resolve ).fail( reject ); + + // Other thenables + } else if ( value && isFunction( ( method = value.then ) ) ) { + method.call( value, resolve, reject ); + + // Other non-thenables + } else { + + // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer: + // * false: [ value ].slice( 0 ) => resolve( value ) + // * true: [ value ].slice( 1 ) => resolve() + resolve.apply( undefined, [ value ].slice( noValue ) ); + } + + // For Promises/A+, convert exceptions into rejections + // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in + // Deferred#then to conditionally suppress rejection. + } catch ( value ) { + + // Support: Android 4.0 only + // Strict mode functions invoked without .call/.apply get global-object context + reject.apply( undefined, [ value ] ); + } +} + +jQuery.extend( { + + Deferred: function( func ) { + var tuples = [ + + // action, add listener, callbacks, + // ... .then handlers, argument index, [final state] + [ "notify", "progress", jQuery.Callbacks( "memory" ), + jQuery.Callbacks( "memory" ), 2 ], + [ "resolve", "done", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 0, "resolved" ], + [ "reject", "fail", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 1, "rejected" ] + ], + state = "pending", + promise = { + state: function() { + return state; + }, + always: function() { + deferred.done( arguments ).fail( arguments ); + return this; + }, + "catch": function( fn ) { + return promise.then( null, fn ); + }, + + // Keep pipe for back-compat + pipe: function( /* fnDone, fnFail, fnProgress */ ) { + var fns = arguments; + + return jQuery.Deferred( function( newDefer ) { + jQuery.each( tuples, function( _i, tuple ) { + + // Map tuples (progress, done, fail) to arguments (done, fail, progress) + var fn = isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ]; + + // deferred.progress(function() { bind to newDefer or newDefer.notify }) + // deferred.done(function() { bind to newDefer or newDefer.resolve }) + // deferred.fail(function() { bind to newDefer or newDefer.reject }) + deferred[ tuple[ 1 ] ]( function() { + var returned = fn && fn.apply( this, arguments ); + if ( returned && isFunction( returned.promise ) ) { + returned.promise() + .progress( newDefer.notify ) + .done( newDefer.resolve ) + .fail( newDefer.reject ); + } else { + newDefer[ tuple[ 0 ] + "With" ]( + this, + fn ? [ returned ] : arguments + ); + } + } ); + } ); + fns = null; + } ).promise(); + }, + then: function( onFulfilled, onRejected, onProgress ) { + var maxDepth = 0; + function resolve( depth, deferred, handler, special ) { + return function() { + var that = this, + args = arguments, + mightThrow = function() { + var returned, then; + + // Support: Promises/A+ section 2.3.3.3.3 + // https://promisesaplus.com/#point-59 + // Ignore double-resolution attempts + if ( depth < maxDepth ) { + return; + } + + returned = handler.apply( that, args ); + + // Support: Promises/A+ section 2.3.1 + // https://promisesaplus.com/#point-48 + if ( returned === deferred.promise() ) { + throw new TypeError( "Thenable self-resolution" ); + } + + // Support: Promises/A+ sections 2.3.3.1, 3.5 + // https://promisesaplus.com/#point-54 + // https://promisesaplus.com/#point-75 + // Retrieve `then` only once + then = returned && + + // Support: Promises/A+ section 2.3.4 + // https://promisesaplus.com/#point-64 + // Only check objects and functions for thenability + ( typeof returned === "object" || + typeof returned === "function" ) && + returned.then; + + // Handle a returned thenable + if ( isFunction( then ) ) { + + // Special processors (notify) just wait for resolution + if ( special ) { + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ) + ); + + // Normal processors (resolve) also hook into progress + } else { + + // ...and disregard older resolution values + maxDepth++; + + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ), + resolve( maxDepth, deferred, Identity, + deferred.notifyWith ) + ); + } + + // Handle all other returned values + } else { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Identity ) { + that = undefined; + args = [ returned ]; + } + + // Process the value(s) + // Default process is resolve + ( special || deferred.resolveWith )( that, args ); + } + }, + + // Only normal processors (resolve) catch and reject exceptions + process = special ? + mightThrow : + function() { + try { + mightThrow(); + } catch ( e ) { + + if ( jQuery.Deferred.exceptionHook ) { + jQuery.Deferred.exceptionHook( e, + process.stackTrace ); + } + + // Support: Promises/A+ section 2.3.3.3.4.1 + // https://promisesaplus.com/#point-61 + // Ignore post-resolution exceptions + if ( depth + 1 >= maxDepth ) { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Thrower ) { + that = undefined; + args = [ e ]; + } + + deferred.rejectWith( that, args ); + } + } + }; + + // Support: Promises/A+ section 2.3.3.3.1 + // https://promisesaplus.com/#point-57 + // Re-resolve promises immediately to dodge false rejection from + // subsequent errors + if ( depth ) { + process(); + } else { + + // Call an optional hook to record the stack, in case of exception + // since it's otherwise lost when execution goes async + if ( jQuery.Deferred.getStackHook ) { + process.stackTrace = jQuery.Deferred.getStackHook(); + } + window.setTimeout( process ); + } + }; + } + + return jQuery.Deferred( function( newDefer ) { + + // progress_handlers.add( ... ) + tuples[ 0 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onProgress ) ? + onProgress : + Identity, + newDefer.notifyWith + ) + ); + + // fulfilled_handlers.add( ... ) + tuples[ 1 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onFulfilled ) ? + onFulfilled : + Identity + ) + ); + + // rejected_handlers.add( ... ) + tuples[ 2 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onRejected ) ? + onRejected : + Thrower + ) + ); + } ).promise(); + }, + + // Get a promise for this deferred + // If obj is provided, the promise aspect is added to the object + promise: function( obj ) { + return obj != null ? jQuery.extend( obj, promise ) : promise; + } + }, + deferred = {}; + + // Add list-specific methods + jQuery.each( tuples, function( i, tuple ) { + var list = tuple[ 2 ], + stateString = tuple[ 5 ]; + + // promise.progress = list.add + // promise.done = list.add + // promise.fail = list.add + promise[ tuple[ 1 ] ] = list.add; + + // Handle state + if ( stateString ) { + list.add( + function() { + + // state = "resolved" (i.e., fulfilled) + // state = "rejected" + state = stateString; + }, + + // rejected_callbacks.disable + // fulfilled_callbacks.disable + tuples[ 3 - i ][ 2 ].disable, + + // rejected_handlers.disable + // fulfilled_handlers.disable + tuples[ 3 - i ][ 3 ].disable, + + // progress_callbacks.lock + tuples[ 0 ][ 2 ].lock, + + // progress_handlers.lock + tuples[ 0 ][ 3 ].lock + ); + } + + // progress_handlers.fire + // fulfilled_handlers.fire + // rejected_handlers.fire + list.add( tuple[ 3 ].fire ); + + // deferred.notify = function() { deferred.notifyWith(...) } + // deferred.resolve = function() { deferred.resolveWith(...) } + // deferred.reject = function() { deferred.rejectWith(...) } + deferred[ tuple[ 0 ] ] = function() { + deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments ); + return this; + }; + + // deferred.notifyWith = list.fireWith + // deferred.resolveWith = list.fireWith + // deferred.rejectWith = list.fireWith + deferred[ tuple[ 0 ] + "With" ] = list.fireWith; + } ); + + // Make the deferred a promise + promise.promise( deferred ); + + // Call given func if any + if ( func ) { + func.call( deferred, deferred ); + } + + // All done! + return deferred; + }, + + // Deferred helper + when: function( singleValue ) { + var + + // count of uncompleted subordinates + remaining = arguments.length, + + // count of unprocessed arguments + i = remaining, + + // subordinate fulfillment data + resolveContexts = Array( i ), + resolveValues = slice.call( arguments ), + + // the master Deferred + master = jQuery.Deferred(), + + // subordinate callback factory + updateFunc = function( i ) { + return function( value ) { + resolveContexts[ i ] = this; + resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value; + if ( !( --remaining ) ) { + master.resolveWith( resolveContexts, resolveValues ); + } + }; + }; + + // Single- and empty arguments are adopted like Promise.resolve + if ( remaining <= 1 ) { + adoptValue( singleValue, master.done( updateFunc( i ) ).resolve, master.reject, + !remaining ); + + // Use .then() to unwrap secondary thenables (cf. gh-3000) + if ( master.state() === "pending" || + isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) { + + return master.then(); + } + } + + // Multiple arguments are aggregated like Promise.all array elements + while ( i-- ) { + adoptValue( resolveValues[ i ], updateFunc( i ), master.reject ); + } + + return master.promise(); + } +} ); + + +// These usually indicate a programmer mistake during development, +// warn about them ASAP rather than swallowing them by default. +var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/; + +jQuery.Deferred.exceptionHook = function( error, stack ) { + + // Support: IE 8 - 9 only + // Console exists when dev tools are open, which can happen at any time + if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) { + window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack ); + } +}; + + + + +jQuery.readyException = function( error ) { + window.setTimeout( function() { + throw error; + } ); +}; + + + + +// The deferred used on DOM ready +var readyList = jQuery.Deferred(); + +jQuery.fn.ready = function( fn ) { + + readyList + .then( fn ) + + // Wrap jQuery.readyException in a function so that the lookup + // happens at the time of error handling instead of callback + // registration. + .catch( function( error ) { + jQuery.readyException( error ); + } ); + + return this; +}; + +jQuery.extend( { + + // Is the DOM ready to be used? Set to true once it occurs. + isReady: false, + + // A counter to track how many items to wait for before + // the ready event fires. See #6781 + readyWait: 1, + + // Handle when the DOM is ready + ready: function( wait ) { + + // Abort if there are pending holds or we're already ready + if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) { + return; + } + + // Remember that the DOM is ready + jQuery.isReady = true; + + // If a normal DOM Ready event fired, decrement, and wait if need be + if ( wait !== true && --jQuery.readyWait > 0 ) { + return; + } + + // If there are functions bound, to execute + readyList.resolveWith( document, [ jQuery ] ); + } +} ); + +jQuery.ready.then = readyList.then; + +// The ready event handler and self cleanup method +function completed() { + document.removeEventListener( "DOMContentLoaded", completed ); + window.removeEventListener( "load", completed ); + jQuery.ready(); +} + +// Catch cases where $(document).ready() is called +// after the browser event has already occurred. +// Support: IE <=9 - 10 only +// Older IE sometimes signals "interactive" too soon +if ( document.readyState === "complete" || + ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) { + + // Handle it asynchronously to allow scripts the opportunity to delay ready + window.setTimeout( jQuery.ready ); + +} else { + + // Use the handy event callback + document.addEventListener( "DOMContentLoaded", completed ); + + // A fallback to window.onload, that will always work + window.addEventListener( "load", completed ); +} + + + + +// Multifunctional method to get and set values of a collection +// The value/s can optionally be executed if it's a function +var access = function( elems, fn, key, value, chainable, emptyGet, raw ) { + var i = 0, + len = elems.length, + bulk = key == null; + + // Sets many values + if ( toType( key ) === "object" ) { + chainable = true; + for ( i in key ) { + access( elems, fn, i, key[ i ], true, emptyGet, raw ); + } + + // Sets one value + } else if ( value !== undefined ) { + chainable = true; + + if ( !isFunction( value ) ) { + raw = true; + } + + if ( bulk ) { + + // Bulk operations run against the entire set + if ( raw ) { + fn.call( elems, value ); + fn = null; + + // ...except when executing function values + } else { + bulk = fn; + fn = function( elem, _key, value ) { + return bulk.call( jQuery( elem ), value ); + }; + } + } + + if ( fn ) { + for ( ; i < len; i++ ) { + fn( + elems[ i ], key, raw ? + value : + value.call( elems[ i ], i, fn( elems[ i ], key ) ) + ); + } + } + } + + if ( chainable ) { + return elems; + } + + // Gets + if ( bulk ) { + return fn.call( elems ); + } + + return len ? fn( elems[ 0 ], key ) : emptyGet; +}; + + +// Matches dashed string for camelizing +var rmsPrefix = /^-ms-/, + rdashAlpha = /-([a-z])/g; + +// Used by camelCase as callback to replace() +function fcamelCase( _all, letter ) { + return letter.toUpperCase(); +} + +// Convert dashed to camelCase; used by the css and data modules +// Support: IE <=9 - 11, Edge 12 - 15 +// Microsoft forgot to hump their vendor prefix (#9572) +function camelCase( string ) { + return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); +} +var acceptData = function( owner ) { + + // Accepts only: + // - Node + // - Node.ELEMENT_NODE + // - Node.DOCUMENT_NODE + // - Object + // - Any + return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType ); +}; + + + + +function Data() { + this.expando = jQuery.expando + Data.uid++; +} + +Data.uid = 1; + +Data.prototype = { + + cache: function( owner ) { + + // Check if the owner object already has a cache + var value = owner[ this.expando ]; + + // If not, create one + if ( !value ) { + value = {}; + + // We can accept data for non-element nodes in modern browsers, + // but we should not, see #8335. + // Always return an empty object. + if ( acceptData( owner ) ) { + + // If it is a node unlikely to be stringify-ed or looped over + // use plain assignment + if ( owner.nodeType ) { + owner[ this.expando ] = value; + + // Otherwise secure it in a non-enumerable property + // configurable must be true to allow the property to be + // deleted when data is removed + } else { + Object.defineProperty( owner, this.expando, { + value: value, + configurable: true + } ); + } + } + } + + return value; + }, + set: function( owner, data, value ) { + var prop, + cache = this.cache( owner ); + + // Handle: [ owner, key, value ] args + // Always use camelCase key (gh-2257) + if ( typeof data === "string" ) { + cache[ camelCase( data ) ] = value; + + // Handle: [ owner, { properties } ] args + } else { + + // Copy the properties one-by-one to the cache object + for ( prop in data ) { + cache[ camelCase( prop ) ] = data[ prop ]; + } + } + return cache; + }, + get: function( owner, key ) { + return key === undefined ? + this.cache( owner ) : + + // Always use camelCase key (gh-2257) + owner[ this.expando ] && owner[ this.expando ][ camelCase( key ) ]; + }, + access: function( owner, key, value ) { + + // In cases where either: + // + // 1. No key was specified + // 2. A string key was specified, but no value provided + // + // Take the "read" path and allow the get method to determine + // which value to return, respectively either: + // + // 1. The entire cache object + // 2. The data stored at the key + // + if ( key === undefined || + ( ( key && typeof key === "string" ) && value === undefined ) ) { + + return this.get( owner, key ); + } + + // When the key is not a string, or both a key and value + // are specified, set or extend (existing objects) with either: + // + // 1. An object of properties + // 2. A key and value + // + this.set( owner, key, value ); + + // Since the "set" path can have two possible entry points + // return the expected data based on which path was taken[*] + return value !== undefined ? value : key; + }, + remove: function( owner, key ) { + var i, + cache = owner[ this.expando ]; + + if ( cache === undefined ) { + return; + } + + if ( key !== undefined ) { + + // Support array or space separated string of keys + if ( Array.isArray( key ) ) { + + // If key is an array of keys... + // We always set camelCase keys, so remove that. + key = key.map( camelCase ); + } else { + key = camelCase( key ); + + // If a key with the spaces exists, use it. + // Otherwise, create an array by matching non-whitespace + key = key in cache ? + [ key ] : + ( key.match( rnothtmlwhite ) || [] ); + } + + i = key.length; + + while ( i-- ) { + delete cache[ key[ i ] ]; + } + } + + // Remove the expando if there's no more data + if ( key === undefined || jQuery.isEmptyObject( cache ) ) { + + // Support: Chrome <=35 - 45 + // Webkit & Blink performance suffers when deleting properties + // from DOM nodes, so set to undefined instead + // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted) + if ( owner.nodeType ) { + owner[ this.expando ] = undefined; + } else { + delete owner[ this.expando ]; + } + } + }, + hasData: function( owner ) { + var cache = owner[ this.expando ]; + return cache !== undefined && !jQuery.isEmptyObject( cache ); + } +}; +var dataPriv = new Data(); + +var dataUser = new Data(); + + + +// Implementation Summary +// +// 1. Enforce API surface and semantic compatibility with 1.9.x branch +// 2. Improve the module's maintainability by reducing the storage +// paths to a single mechanism. +// 3. Use the same single mechanism to support "private" and "user" data. +// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData) +// 5. Avoid exposing implementation details on user objects (eg. expando properties) +// 6. Provide a clear path for implementation upgrade to WeakMap in 2014 + +var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/, + rmultiDash = /[A-Z]/g; + +function getData( data ) { + if ( data === "true" ) { + return true; + } + + if ( data === "false" ) { + return false; + } + + if ( data === "null" ) { + return null; + } + + // Only convert to a number if it doesn't change the string + if ( data === +data + "" ) { + return +data; + } + + if ( rbrace.test( data ) ) { + return JSON.parse( data ); + } + + return data; +} + +function dataAttr( elem, key, data ) { + var name; + + // If nothing was found internally, try to fetch any + // data from the HTML5 data-* attribute + if ( data === undefined && elem.nodeType === 1 ) { + name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase(); + data = elem.getAttribute( name ); + + if ( typeof data === "string" ) { + try { + data = getData( data ); + } catch ( e ) {} + + // Make sure we set the data so it isn't changed later + dataUser.set( elem, key, data ); + } else { + data = undefined; + } + } + return data; +} + +jQuery.extend( { + hasData: function( elem ) { + return dataUser.hasData( elem ) || dataPriv.hasData( elem ); + }, + + data: function( elem, name, data ) { + return dataUser.access( elem, name, data ); + }, + + removeData: function( elem, name ) { + dataUser.remove( elem, name ); + }, + + // TODO: Now that all calls to _data and _removeData have been replaced + // with direct calls to dataPriv methods, these can be deprecated. + _data: function( elem, name, data ) { + return dataPriv.access( elem, name, data ); + }, + + _removeData: function( elem, name ) { + dataPriv.remove( elem, name ); + } +} ); + +jQuery.fn.extend( { + data: function( key, value ) { + var i, name, data, + elem = this[ 0 ], + attrs = elem && elem.attributes; + + // Gets all values + if ( key === undefined ) { + if ( this.length ) { + data = dataUser.get( elem ); + + if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) { + i = attrs.length; + while ( i-- ) { + + // Support: IE 11 only + // The attrs elements can be null (#14894) + if ( attrs[ i ] ) { + name = attrs[ i ].name; + if ( name.indexOf( "data-" ) === 0 ) { + name = camelCase( name.slice( 5 ) ); + dataAttr( elem, name, data[ name ] ); + } + } + } + dataPriv.set( elem, "hasDataAttrs", true ); + } + } + + return data; + } + + // Sets multiple values + if ( typeof key === "object" ) { + return this.each( function() { + dataUser.set( this, key ); + } ); + } + + return access( this, function( value ) { + var data; + + // The calling jQuery object (element matches) is not empty + // (and therefore has an element appears at this[ 0 ]) and the + // `value` parameter was not undefined. An empty jQuery object + // will result in `undefined` for elem = this[ 0 ] which will + // throw an exception if an attempt to read a data cache is made. + if ( elem && value === undefined ) { + + // Attempt to get data from the cache + // The key will always be camelCased in Data + data = dataUser.get( elem, key ); + if ( data !== undefined ) { + return data; + } + + // Attempt to "discover" the data in + // HTML5 custom data-* attrs + data = dataAttr( elem, key ); + if ( data !== undefined ) { + return data; + } + + // We tried really hard, but the data doesn't exist. + return; + } + + // Set the data... + this.each( function() { + + // We always store the camelCased key + dataUser.set( this, key, value ); + } ); + }, null, value, arguments.length > 1, null, true ); + }, + + removeData: function( key ) { + return this.each( function() { + dataUser.remove( this, key ); + } ); + } +} ); + + +jQuery.extend( { + queue: function( elem, type, data ) { + var queue; + + if ( elem ) { + type = ( type || "fx" ) + "queue"; + queue = dataPriv.get( elem, type ); + + // Speed up dequeue by getting out quickly if this is just a lookup + if ( data ) { + if ( !queue || Array.isArray( data ) ) { + queue = dataPriv.access( elem, type, jQuery.makeArray( data ) ); + } else { + queue.push( data ); + } + } + return queue || []; + } + }, + + dequeue: function( elem, type ) { + type = type || "fx"; + + var queue = jQuery.queue( elem, type ), + startLength = queue.length, + fn = queue.shift(), + hooks = jQuery._queueHooks( elem, type ), + next = function() { + jQuery.dequeue( elem, type ); + }; + + // If the fx queue is dequeued, always remove the progress sentinel + if ( fn === "inprogress" ) { + fn = queue.shift(); + startLength--; + } + + if ( fn ) { + + // Add a progress sentinel to prevent the fx queue from being + // automatically dequeued + if ( type === "fx" ) { + queue.unshift( "inprogress" ); + } + + // Clear up the last queue stop function + delete hooks.stop; + fn.call( elem, next, hooks ); + } + + if ( !startLength && hooks ) { + hooks.empty.fire(); + } + }, + + // Not public - generate a queueHooks object, or return the current one + _queueHooks: function( elem, type ) { + var key = type + "queueHooks"; + return dataPriv.get( elem, key ) || dataPriv.access( elem, key, { + empty: jQuery.Callbacks( "once memory" ).add( function() { + dataPriv.remove( elem, [ type + "queue", key ] ); + } ) + } ); + } +} ); + +jQuery.fn.extend( { + queue: function( type, data ) { + var setter = 2; + + if ( typeof type !== "string" ) { + data = type; + type = "fx"; + setter--; + } + + if ( arguments.length < setter ) { + return jQuery.queue( this[ 0 ], type ); + } + + return data === undefined ? + this : + this.each( function() { + var queue = jQuery.queue( this, type, data ); + + // Ensure a hooks for this queue + jQuery._queueHooks( this, type ); + + if ( type === "fx" && queue[ 0 ] !== "inprogress" ) { + jQuery.dequeue( this, type ); + } + } ); + }, + dequeue: function( type ) { + return this.each( function() { + jQuery.dequeue( this, type ); + } ); + }, + clearQueue: function( type ) { + return this.queue( type || "fx", [] ); + }, + + // Get a promise resolved when queues of a certain type + // are emptied (fx is the type by default) + promise: function( type, obj ) { + var tmp, + count = 1, + defer = jQuery.Deferred(), + elements = this, + i = this.length, + resolve = function() { + if ( !( --count ) ) { + defer.resolveWith( elements, [ elements ] ); + } + }; + + if ( typeof type !== "string" ) { + obj = type; + type = undefined; + } + type = type || "fx"; + + while ( i-- ) { + tmp = dataPriv.get( elements[ i ], type + "queueHooks" ); + if ( tmp && tmp.empty ) { + count++; + tmp.empty.add( resolve ); + } + } + resolve(); + return defer.promise( obj ); + } +} ); +var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source; + +var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ); + + +var cssExpand = [ "Top", "Right", "Bottom", "Left" ]; + +var documentElement = document.documentElement; + + + + var isAttached = function( elem ) { + return jQuery.contains( elem.ownerDocument, elem ); + }, + composed = { composed: true }; + + // Support: IE 9 - 11+, Edge 12 - 18+, iOS 10.0 - 10.2 only + // Check attachment across shadow DOM boundaries when possible (gh-3504) + // Support: iOS 10.0-10.2 only + // Early iOS 10 versions support `attachShadow` but not `getRootNode`, + // leading to errors. We need to check for `getRootNode`. + if ( documentElement.getRootNode ) { + isAttached = function( elem ) { + return jQuery.contains( elem.ownerDocument, elem ) || + elem.getRootNode( composed ) === elem.ownerDocument; + }; + } +var isHiddenWithinTree = function( elem, el ) { + + // isHiddenWithinTree might be called from jQuery#filter function; + // in that case, element will be second argument + elem = el || elem; + + // Inline style trumps all + return elem.style.display === "none" || + elem.style.display === "" && + + // Otherwise, check computed style + // Support: Firefox <=43 - 45 + // Disconnected elements can have computed display: none, so first confirm that elem is + // in the document. + isAttached( elem ) && + + jQuery.css( elem, "display" ) === "none"; + }; + + + +function adjustCSS( elem, prop, valueParts, tween ) { + var adjusted, scale, + maxIterations = 20, + currentValue = tween ? + function() { + return tween.cur(); + } : + function() { + return jQuery.css( elem, prop, "" ); + }, + initial = currentValue(), + unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ), + + // Starting value computation is required for potential unit mismatches + initialInUnit = elem.nodeType && + ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) && + rcssNum.exec( jQuery.css( elem, prop ) ); + + if ( initialInUnit && initialInUnit[ 3 ] !== unit ) { + + // Support: Firefox <=54 + // Halve the iteration target value to prevent interference from CSS upper bounds (gh-2144) + initial = initial / 2; + + // Trust units reported by jQuery.css + unit = unit || initialInUnit[ 3 ]; + + // Iteratively approximate from a nonzero starting point + initialInUnit = +initial || 1; + + while ( maxIterations-- ) { + + // Evaluate and update our best guess (doubling guesses that zero out). + // Finish if the scale equals or crosses 1 (making the old*new product non-positive). + jQuery.style( elem, prop, initialInUnit + unit ); + if ( ( 1 - scale ) * ( 1 - ( scale = currentValue() / initial || 0.5 ) ) <= 0 ) { + maxIterations = 0; + } + initialInUnit = initialInUnit / scale; + + } + + initialInUnit = initialInUnit * 2; + jQuery.style( elem, prop, initialInUnit + unit ); + + // Make sure we update the tween properties later on + valueParts = valueParts || []; + } + + if ( valueParts ) { + initialInUnit = +initialInUnit || +initial || 0; + + // Apply relative offset (+=/-=) if specified + adjusted = valueParts[ 1 ] ? + initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] : + +valueParts[ 2 ]; + if ( tween ) { + tween.unit = unit; + tween.start = initialInUnit; + tween.end = adjusted; + } + } + return adjusted; +} + + +var defaultDisplayMap = {}; + +function getDefaultDisplay( elem ) { + var temp, + doc = elem.ownerDocument, + nodeName = elem.nodeName, + display = defaultDisplayMap[ nodeName ]; + + if ( display ) { + return display; + } + + temp = doc.body.appendChild( doc.createElement( nodeName ) ); + display = jQuery.css( temp, "display" ); + + temp.parentNode.removeChild( temp ); + + if ( display === "none" ) { + display = "block"; + } + defaultDisplayMap[ nodeName ] = display; + + return display; +} + +function showHide( elements, show ) { + var display, elem, + values = [], + index = 0, + length = elements.length; + + // Determine new display value for elements that need to change + for ( ; index < length; index++ ) { + elem = elements[ index ]; + if ( !elem.style ) { + continue; + } + + display = elem.style.display; + if ( show ) { + + // Since we force visibility upon cascade-hidden elements, an immediate (and slow) + // check is required in this first loop unless we have a nonempty display value (either + // inline or about-to-be-restored) + if ( display === "none" ) { + values[ index ] = dataPriv.get( elem, "display" ) || null; + if ( !values[ index ] ) { + elem.style.display = ""; + } + } + if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) { + values[ index ] = getDefaultDisplay( elem ); + } + } else { + if ( display !== "none" ) { + values[ index ] = "none"; + + // Remember what we're overwriting + dataPriv.set( elem, "display", display ); + } + } + } + + // Set the display of the elements in a second loop to avoid constant reflow + for ( index = 0; index < length; index++ ) { + if ( values[ index ] != null ) { + elements[ index ].style.display = values[ index ]; + } + } + + return elements; +} + +jQuery.fn.extend( { + show: function() { + return showHide( this, true ); + }, + hide: function() { + return showHide( this ); + }, + toggle: function( state ) { + if ( typeof state === "boolean" ) { + return state ? this.show() : this.hide(); + } + + return this.each( function() { + if ( isHiddenWithinTree( this ) ) { + jQuery( this ).show(); + } else { + jQuery( this ).hide(); + } + } ); + } +} ); +var rcheckableType = ( /^(?:checkbox|radio)$/i ); + +var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]*)/i ); + +var rscriptType = ( /^$|^module$|\/(?:java|ecma)script/i ); + + + +( function() { + var fragment = document.createDocumentFragment(), + div = fragment.appendChild( document.createElement( "div" ) ), + input = document.createElement( "input" ); + + // Support: Android 4.0 - 4.3 only + // Check state lost if the name is set (#11217) + // Support: Windows Web Apps (WWA) + // `name` and `type` must use .setAttribute for WWA (#14901) + input.setAttribute( "type", "radio" ); + input.setAttribute( "checked", "checked" ); + input.setAttribute( "name", "t" ); + + div.appendChild( input ); + + // Support: Android <=4.1 only + // Older WebKit doesn't clone checked state correctly in fragments + support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked; + + // Support: IE <=11 only + // Make sure textarea (and checkbox) defaultValue is properly cloned + div.innerHTML = ""; + support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue; + + // Support: IE <=9 only + // IE <=9 replaces "; + support.option = !!div.lastChild; +} )(); + + +// We have to close these tags to support XHTML (#13200) +var wrapMap = { + + // XHTML parsers do not magically insert elements in the + // same way that tag soup parsers do. So we cannot shorten + // this by omitting or other required elements. + thead: [ 1, "", "
" ], + col: [ 2, "", "
" ], + tr: [ 2, "", "
" ], + td: [ 3, "", "
" ], + + _default: [ 0, "", "" ] +}; + +wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; +wrapMap.th = wrapMap.td; + +// Support: IE <=9 only +if ( !support.option ) { + wrapMap.optgroup = wrapMap.option = [ 1, "" ]; +} + + +function getAll( context, tag ) { + + // Support: IE <=9 - 11 only + // Use typeof to avoid zero-argument method invocation on host objects (#15151) + var ret; + + if ( typeof context.getElementsByTagName !== "undefined" ) { + ret = context.getElementsByTagName( tag || "*" ); + + } else if ( typeof context.querySelectorAll !== "undefined" ) { + ret = context.querySelectorAll( tag || "*" ); + + } else { + ret = []; + } + + if ( tag === undefined || tag && nodeName( context, tag ) ) { + return jQuery.merge( [ context ], ret ); + } + + return ret; +} + + +// Mark scripts as having already been evaluated +function setGlobalEval( elems, refElements ) { + var i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + dataPriv.set( + elems[ i ], + "globalEval", + !refElements || dataPriv.get( refElements[ i ], "globalEval" ) + ); + } +} + + +var rhtml = /<|&#?\w+;/; + +function buildFragment( elems, context, scripts, selection, ignored ) { + var elem, tmp, tag, wrap, attached, j, + fragment = context.createDocumentFragment(), + nodes = [], + i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + elem = elems[ i ]; + + if ( elem || elem === 0 ) { + + // Add nodes directly + if ( toType( elem ) === "object" ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem ); + + // Convert non-html into a text node + } else if ( !rhtml.test( elem ) ) { + nodes.push( context.createTextNode( elem ) ); + + // Convert html into DOM nodes + } else { + tmp = tmp || fragment.appendChild( context.createElement( "div" ) ); + + // Deserialize a standard representation + tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase(); + wrap = wrapMap[ tag ] || wrapMap._default; + tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ]; + + // Descend through wrappers to the right content + j = wrap[ 0 ]; + while ( j-- ) { + tmp = tmp.lastChild; + } + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, tmp.childNodes ); + + // Remember the top-level container + tmp = fragment.firstChild; + + // Ensure the created nodes are orphaned (#12392) + tmp.textContent = ""; + } + } + } + + // Remove wrapper from fragment + fragment.textContent = ""; + + i = 0; + while ( ( elem = nodes[ i++ ] ) ) { + + // Skip elements already in the context collection (trac-4087) + if ( selection && jQuery.inArray( elem, selection ) > -1 ) { + if ( ignored ) { + ignored.push( elem ); + } + continue; + } + + attached = isAttached( elem ); + + // Append to fragment + tmp = getAll( fragment.appendChild( elem ), "script" ); + + // Preserve script evaluation history + if ( attached ) { + setGlobalEval( tmp ); + } + + // Capture executables + if ( scripts ) { + j = 0; + while ( ( elem = tmp[ j++ ] ) ) { + if ( rscriptType.test( elem.type || "" ) ) { + scripts.push( elem ); + } + } + } + } + + return fragment; +} + + +var + rkeyEvent = /^key/, + rmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/, + rtypenamespace = /^([^.]*)(?:\.(.+)|)/; + +function returnTrue() { + return true; +} + +function returnFalse() { + return false; +} + +// Support: IE <=9 - 11+ +// focus() and blur() are asynchronous, except when they are no-op. +// So expect focus to be synchronous when the element is already active, +// and blur to be synchronous when the element is not already active. +// (focus and blur are always synchronous in other supported browsers, +// this just defines when we can count on it). +function expectSync( elem, type ) { + return ( elem === safeActiveElement() ) === ( type === "focus" ); +} + +// Support: IE <=9 only +// Accessing document.activeElement can throw unexpectedly +// https://bugs.jquery.com/ticket/13393 +function safeActiveElement() { + try { + return document.activeElement; + } catch ( err ) { } +} + +function on( elem, types, selector, data, fn, one ) { + var origFn, type; + + // Types can be a map of types/handlers + if ( typeof types === "object" ) { + + // ( types-Object, selector, data ) + if ( typeof selector !== "string" ) { + + // ( types-Object, data ) + data = data || selector; + selector = undefined; + } + for ( type in types ) { + on( elem, type, selector, data, types[ type ], one ); + } + return elem; + } + + if ( data == null && fn == null ) { + + // ( types, fn ) + fn = selector; + data = selector = undefined; + } else if ( fn == null ) { + if ( typeof selector === "string" ) { + + // ( types, selector, fn ) + fn = data; + data = undefined; + } else { + + // ( types, data, fn ) + fn = data; + data = selector; + selector = undefined; + } + } + if ( fn === false ) { + fn = returnFalse; + } else if ( !fn ) { + return elem; + } + + if ( one === 1 ) { + origFn = fn; + fn = function( event ) { + + // Can use an empty set, since event contains the info + jQuery().off( event ); + return origFn.apply( this, arguments ); + }; + + // Use same guid so caller can remove using origFn + fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); + } + return elem.each( function() { + jQuery.event.add( this, types, fn, data, selector ); + } ); +} + +/* + * Helper functions for managing events -- not part of the public interface. + * Props to Dean Edwards' addEvent library for many of the ideas. + */ +jQuery.event = { + + global: {}, + + add: function( elem, types, handler, data, selector ) { + + var handleObjIn, eventHandle, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.get( elem ); + + // Only attach events to objects that accept data + if ( !acceptData( elem ) ) { + return; + } + + // Caller can pass in an object of custom data in lieu of the handler + if ( handler.handler ) { + handleObjIn = handler; + handler = handleObjIn.handler; + selector = handleObjIn.selector; + } + + // Ensure that invalid selectors throw exceptions at attach time + // Evaluate against documentElement in case elem is a non-element node (e.g., document) + if ( selector ) { + jQuery.find.matchesSelector( documentElement, selector ); + } + + // Make sure that the handler has a unique ID, used to find/remove it later + if ( !handler.guid ) { + handler.guid = jQuery.guid++; + } + + // Init the element's event structure and main handler, if this is the first + if ( !( events = elemData.events ) ) { + events = elemData.events = Object.create( null ); + } + if ( !( eventHandle = elemData.handle ) ) { + eventHandle = elemData.handle = function( e ) { + + // Discard the second event of a jQuery.event.trigger() and + // when an event is called after a page has unloaded + return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? + jQuery.event.dispatch.apply( elem, arguments ) : undefined; + }; + } + + // Handle multiple events separated by a space + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // There *must* be a type, no attaching namespace-only handlers + if ( !type ) { + continue; + } + + // If event changes its type, use the special event handlers for the changed type + special = jQuery.event.special[ type ] || {}; + + // If selector defined, determine special event api type, otherwise given type + type = ( selector ? special.delegateType : special.bindType ) || type; + + // Update special based on newly reset type + special = jQuery.event.special[ type ] || {}; + + // handleObj is passed to all event handlers + handleObj = jQuery.extend( { + type: type, + origType: origType, + data: data, + handler: handler, + guid: handler.guid, + selector: selector, + needsContext: selector && jQuery.expr.match.needsContext.test( selector ), + namespace: namespaces.join( "." ) + }, handleObjIn ); + + // Init the event handler queue if we're the first + if ( !( handlers = events[ type ] ) ) { + handlers = events[ type ] = []; + handlers.delegateCount = 0; + + // Only use addEventListener if the special events handler returns false + if ( !special.setup || + special.setup.call( elem, data, namespaces, eventHandle ) === false ) { + + if ( elem.addEventListener ) { + elem.addEventListener( type, eventHandle ); + } + } + } + + if ( special.add ) { + special.add.call( elem, handleObj ); + + if ( !handleObj.handler.guid ) { + handleObj.handler.guid = handler.guid; + } + } + + // Add to the element's handler list, delegates in front + if ( selector ) { + handlers.splice( handlers.delegateCount++, 0, handleObj ); + } else { + handlers.push( handleObj ); + } + + // Keep track of which events have ever been used, for event optimization + jQuery.event.global[ type ] = true; + } + + }, + + // Detach an event or set of events from an element + remove: function( elem, types, handler, selector, mappedTypes ) { + + var j, origCount, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.hasData( elem ) && dataPriv.get( elem ); + + if ( !elemData || !( events = elemData.events ) ) { + return; + } + + // Once for each type.namespace in types; type may be omitted + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // Unbind all events (on this namespace, if provided) for the element + if ( !type ) { + for ( type in events ) { + jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); + } + continue; + } + + special = jQuery.event.special[ type ] || {}; + type = ( selector ? special.delegateType : special.bindType ) || type; + handlers = events[ type ] || []; + tmp = tmp[ 2 ] && + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ); + + // Remove matching events + origCount = j = handlers.length; + while ( j-- ) { + handleObj = handlers[ j ]; + + if ( ( mappedTypes || origType === handleObj.origType ) && + ( !handler || handler.guid === handleObj.guid ) && + ( !tmp || tmp.test( handleObj.namespace ) ) && + ( !selector || selector === handleObj.selector || + selector === "**" && handleObj.selector ) ) { + handlers.splice( j, 1 ); + + if ( handleObj.selector ) { + handlers.delegateCount--; + } + if ( special.remove ) { + special.remove.call( elem, handleObj ); + } + } + } + + // Remove generic event handler if we removed something and no more handlers exist + // (avoids potential for endless recursion during removal of special event handlers) + if ( origCount && !handlers.length ) { + if ( !special.teardown || + special.teardown.call( elem, namespaces, elemData.handle ) === false ) { + + jQuery.removeEvent( elem, type, elemData.handle ); + } + + delete events[ type ]; + } + } + + // Remove data and the expando if it's no longer used + if ( jQuery.isEmptyObject( events ) ) { + dataPriv.remove( elem, "handle events" ); + } + }, + + dispatch: function( nativeEvent ) { + + var i, j, ret, matched, handleObj, handlerQueue, + args = new Array( arguments.length ), + + // Make a writable jQuery.Event from the native event object + event = jQuery.event.fix( nativeEvent ), + + handlers = ( + dataPriv.get( this, "events" ) || Object.create( null ) + )[ event.type ] || [], + special = jQuery.event.special[ event.type ] || {}; + + // Use the fix-ed jQuery.Event rather than the (read-only) native event + args[ 0 ] = event; + + for ( i = 1; i < arguments.length; i++ ) { + args[ i ] = arguments[ i ]; + } + + event.delegateTarget = this; + + // Call the preDispatch hook for the mapped type, and let it bail if desired + if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { + return; + } + + // Determine handlers + handlerQueue = jQuery.event.handlers.call( this, event, handlers ); + + // Run delegates first; they may want to stop propagation beneath us + i = 0; + while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) { + event.currentTarget = matched.elem; + + j = 0; + while ( ( handleObj = matched.handlers[ j++ ] ) && + !event.isImmediatePropagationStopped() ) { + + // If the event is namespaced, then each handler is only invoked if it is + // specially universal or its namespaces are a superset of the event's. + if ( !event.rnamespace || handleObj.namespace === false || + event.rnamespace.test( handleObj.namespace ) ) { + + event.handleObj = handleObj; + event.data = handleObj.data; + + ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle || + handleObj.handler ).apply( matched.elem, args ); + + if ( ret !== undefined ) { + if ( ( event.result = ret ) === false ) { + event.preventDefault(); + event.stopPropagation(); + } + } + } + } + } + + // Call the postDispatch hook for the mapped type + if ( special.postDispatch ) { + special.postDispatch.call( this, event ); + } + + return event.result; + }, + + handlers: function( event, handlers ) { + var i, handleObj, sel, matchedHandlers, matchedSelectors, + handlerQueue = [], + delegateCount = handlers.delegateCount, + cur = event.target; + + // Find delegate handlers + if ( delegateCount && + + // Support: IE <=9 + // Black-hole SVG instance trees (trac-13180) + cur.nodeType && + + // Support: Firefox <=42 + // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861) + // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click + // Support: IE 11 only + // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343) + !( event.type === "click" && event.button >= 1 ) ) { + + for ( ; cur !== this; cur = cur.parentNode || this ) { + + // Don't check non-elements (#13208) + // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) + if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) { + matchedHandlers = []; + matchedSelectors = {}; + for ( i = 0; i < delegateCount; i++ ) { + handleObj = handlers[ i ]; + + // Don't conflict with Object.prototype properties (#13203) + sel = handleObj.selector + " "; + + if ( matchedSelectors[ sel ] === undefined ) { + matchedSelectors[ sel ] = handleObj.needsContext ? + jQuery( sel, this ).index( cur ) > -1 : + jQuery.find( sel, this, null, [ cur ] ).length; + } + if ( matchedSelectors[ sel ] ) { + matchedHandlers.push( handleObj ); + } + } + if ( matchedHandlers.length ) { + handlerQueue.push( { elem: cur, handlers: matchedHandlers } ); + } + } + } + } + + // Add the remaining (directly-bound) handlers + cur = this; + if ( delegateCount < handlers.length ) { + handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } ); + } + + return handlerQueue; + }, + + addProp: function( name, hook ) { + Object.defineProperty( jQuery.Event.prototype, name, { + enumerable: true, + configurable: true, + + get: isFunction( hook ) ? + function() { + if ( this.originalEvent ) { + return hook( this.originalEvent ); + } + } : + function() { + if ( this.originalEvent ) { + return this.originalEvent[ name ]; + } + }, + + set: function( value ) { + Object.defineProperty( this, name, { + enumerable: true, + configurable: true, + writable: true, + value: value + } ); + } + } ); + }, + + fix: function( originalEvent ) { + return originalEvent[ jQuery.expando ] ? + originalEvent : + new jQuery.Event( originalEvent ); + }, + + special: { + load: { + + // Prevent triggered image.load events from bubbling to window.load + noBubble: true + }, + click: { + + // Utilize native event to ensure correct state for checkable inputs + setup: function( data ) { + + // For mutual compressibility with _default, replace `this` access with a local var. + // `|| data` is dead code meant only to preserve the variable through minification. + var el = this || data; + + // Claim the first handler + if ( rcheckableType.test( el.type ) && + el.click && nodeName( el, "input" ) ) { + + // dataPriv.set( el, "click", ... ) + leverageNative( el, "click", returnTrue ); + } + + // Return false to allow normal processing in the caller + return false; + }, + trigger: function( data ) { + + // For mutual compressibility with _default, replace `this` access with a local var. + // `|| data` is dead code meant only to preserve the variable through minification. + var el = this || data; + + // Force setup before triggering a click + if ( rcheckableType.test( el.type ) && + el.click && nodeName( el, "input" ) ) { + + leverageNative( el, "click" ); + } + + // Return non-false to allow normal event-path propagation + return true; + }, + + // For cross-browser consistency, suppress native .click() on links + // Also prevent it if we're currently inside a leveraged native-event stack + _default: function( event ) { + var target = event.target; + return rcheckableType.test( target.type ) && + target.click && nodeName( target, "input" ) && + dataPriv.get( target, "click" ) || + nodeName( target, "a" ); + } + }, + + beforeunload: { + postDispatch: function( event ) { + + // Support: Firefox 20+ + // Firefox doesn't alert if the returnValue field is not set. + if ( event.result !== undefined && event.originalEvent ) { + event.originalEvent.returnValue = event.result; + } + } + } + } +}; + +// Ensure the presence of an event listener that handles manually-triggered +// synthetic events by interrupting progress until reinvoked in response to +// *native* events that it fires directly, ensuring that state changes have +// already occurred before other listeners are invoked. +function leverageNative( el, type, expectSync ) { + + // Missing expectSync indicates a trigger call, which must force setup through jQuery.event.add + if ( !expectSync ) { + if ( dataPriv.get( el, type ) === undefined ) { + jQuery.event.add( el, type, returnTrue ); + } + return; + } + + // Register the controller as a special universal handler for all event namespaces + dataPriv.set( el, type, false ); + jQuery.event.add( el, type, { + namespace: false, + handler: function( event ) { + var notAsync, result, + saved = dataPriv.get( this, type ); + + if ( ( event.isTrigger & 1 ) && this[ type ] ) { + + // Interrupt processing of the outer synthetic .trigger()ed event + // Saved data should be false in such cases, but might be a leftover capture object + // from an async native handler (gh-4350) + if ( !saved.length ) { + + // Store arguments for use when handling the inner native event + // There will always be at least one argument (an event object), so this array + // will not be confused with a leftover capture object. + saved = slice.call( arguments ); + dataPriv.set( this, type, saved ); + + // Trigger the native event and capture its result + // Support: IE <=9 - 11+ + // focus() and blur() are asynchronous + notAsync = expectSync( this, type ); + this[ type ](); + result = dataPriv.get( this, type ); + if ( saved !== result || notAsync ) { + dataPriv.set( this, type, false ); + } else { + result = {}; + } + if ( saved !== result ) { + + // Cancel the outer synthetic event + event.stopImmediatePropagation(); + event.preventDefault(); + return result.value; + } + + // If this is an inner synthetic event for an event with a bubbling surrogate + // (focus or blur), assume that the surrogate already propagated from triggering the + // native event and prevent that from happening again here. + // This technically gets the ordering wrong w.r.t. to `.trigger()` (in which the + // bubbling surrogate propagates *after* the non-bubbling base), but that seems + // less bad than duplication. + } else if ( ( jQuery.event.special[ type ] || {} ).delegateType ) { + event.stopPropagation(); + } + + // If this is a native event triggered above, everything is now in order + // Fire an inner synthetic event with the original arguments + } else if ( saved.length ) { + + // ...and capture the result + dataPriv.set( this, type, { + value: jQuery.event.trigger( + + // Support: IE <=9 - 11+ + // Extend with the prototype to reset the above stopImmediatePropagation() + jQuery.extend( saved[ 0 ], jQuery.Event.prototype ), + saved.slice( 1 ), + this + ) + } ); + + // Abort handling of the native event + event.stopImmediatePropagation(); + } + } + } ); +} + +jQuery.removeEvent = function( elem, type, handle ) { + + // This "if" is needed for plain objects + if ( elem.removeEventListener ) { + elem.removeEventListener( type, handle ); + } +}; + +jQuery.Event = function( src, props ) { + + // Allow instantiation without the 'new' keyword + if ( !( this instanceof jQuery.Event ) ) { + return new jQuery.Event( src, props ); + } + + // Event object + if ( src && src.type ) { + this.originalEvent = src; + this.type = src.type; + + // Events bubbling up the document may have been marked as prevented + // by a handler lower down the tree; reflect the correct value. + this.isDefaultPrevented = src.defaultPrevented || + src.defaultPrevented === undefined && + + // Support: Android <=2.3 only + src.returnValue === false ? + returnTrue : + returnFalse; + + // Create target properties + // Support: Safari <=6 - 7 only + // Target should not be a text node (#504, #13143) + this.target = ( src.target && src.target.nodeType === 3 ) ? + src.target.parentNode : + src.target; + + this.currentTarget = src.currentTarget; + this.relatedTarget = src.relatedTarget; + + // Event type + } else { + this.type = src; + } + + // Put explicitly provided properties onto the event object + if ( props ) { + jQuery.extend( this, props ); + } + + // Create a timestamp if incoming event doesn't have one + this.timeStamp = src && src.timeStamp || Date.now(); + + // Mark it as fixed + this[ jQuery.expando ] = true; +}; + +// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding +// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html +jQuery.Event.prototype = { + constructor: jQuery.Event, + isDefaultPrevented: returnFalse, + isPropagationStopped: returnFalse, + isImmediatePropagationStopped: returnFalse, + isSimulated: false, + + preventDefault: function() { + var e = this.originalEvent; + + this.isDefaultPrevented = returnTrue; + + if ( e && !this.isSimulated ) { + e.preventDefault(); + } + }, + stopPropagation: function() { + var e = this.originalEvent; + + this.isPropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopPropagation(); + } + }, + stopImmediatePropagation: function() { + var e = this.originalEvent; + + this.isImmediatePropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopImmediatePropagation(); + } + + this.stopPropagation(); + } +}; + +// Includes all common event props including KeyEvent and MouseEvent specific props +jQuery.each( { + altKey: true, + bubbles: true, + cancelable: true, + changedTouches: true, + ctrlKey: true, + detail: true, + eventPhase: true, + metaKey: true, + pageX: true, + pageY: true, + shiftKey: true, + view: true, + "char": true, + code: true, + charCode: true, + key: true, + keyCode: true, + button: true, + buttons: true, + clientX: true, + clientY: true, + offsetX: true, + offsetY: true, + pointerId: true, + pointerType: true, + screenX: true, + screenY: true, + targetTouches: true, + toElement: true, + touches: true, + + which: function( event ) { + var button = event.button; + + // Add which for key events + if ( event.which == null && rkeyEvent.test( event.type ) ) { + return event.charCode != null ? event.charCode : event.keyCode; + } + + // Add which for click: 1 === left; 2 === middle; 3 === right + if ( !event.which && button !== undefined && rmouseEvent.test( event.type ) ) { + if ( button & 1 ) { + return 1; + } + + if ( button & 2 ) { + return 3; + } + + if ( button & 4 ) { + return 2; + } + + return 0; + } + + return event.which; + } +}, jQuery.event.addProp ); + +jQuery.each( { focus: "focusin", blur: "focusout" }, function( type, delegateType ) { + jQuery.event.special[ type ] = { + + // Utilize native event if possible so blur/focus sequence is correct + setup: function() { + + // Claim the first handler + // dataPriv.set( this, "focus", ... ) + // dataPriv.set( this, "blur", ... ) + leverageNative( this, type, expectSync ); + + // Return false to allow normal processing in the caller + return false; + }, + trigger: function() { + + // Force setup before trigger + leverageNative( this, type ); + + // Return non-false to allow normal event-path propagation + return true; + }, + + delegateType: delegateType + }; +} ); + +// Create mouseenter/leave events using mouseover/out and event-time checks +// so that event delegation works in jQuery. +// Do the same for pointerenter/pointerleave and pointerover/pointerout +// +// Support: Safari 7 only +// Safari sends mouseenter too often; see: +// https://bugs.chromium.org/p/chromium/issues/detail?id=470258 +// for the description of the bug (it existed in older Chrome versions as well). +jQuery.each( { + mouseenter: "mouseover", + mouseleave: "mouseout", + pointerenter: "pointerover", + pointerleave: "pointerout" +}, function( orig, fix ) { + jQuery.event.special[ orig ] = { + delegateType: fix, + bindType: fix, + + handle: function( event ) { + var ret, + target = this, + related = event.relatedTarget, + handleObj = event.handleObj; + + // For mouseenter/leave call the handler if related is outside the target. + // NB: No relatedTarget if the mouse left/entered the browser window + if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) { + event.type = handleObj.origType; + ret = handleObj.handler.apply( this, arguments ); + event.type = fix; + } + return ret; + } + }; +} ); + +jQuery.fn.extend( { + + on: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn ); + }, + one: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn, 1 ); + }, + off: function( types, selector, fn ) { + var handleObj, type; + if ( types && types.preventDefault && types.handleObj ) { + + // ( event ) dispatched jQuery.Event + handleObj = types.handleObj; + jQuery( types.delegateTarget ).off( + handleObj.namespace ? + handleObj.origType + "." + handleObj.namespace : + handleObj.origType, + handleObj.selector, + handleObj.handler + ); + return this; + } + if ( typeof types === "object" ) { + + // ( types-object [, selector] ) + for ( type in types ) { + this.off( type, selector, types[ type ] ); + } + return this; + } + if ( selector === false || typeof selector === "function" ) { + + // ( types [, fn] ) + fn = selector; + selector = undefined; + } + if ( fn === false ) { + fn = returnFalse; + } + return this.each( function() { + jQuery.event.remove( this, types, fn, selector ); + } ); + } +} ); + + +var + + // Support: IE <=10 - 11, Edge 12 - 13 only + // In IE/Edge using regex groups here causes severe slowdowns. + // See https://connect.microsoft.com/IE/feedback/details/1736512/ + rnoInnerhtml = /\s*$/g; + +// Prefer a tbody over its parent table for containing new rows +function manipulationTarget( elem, content ) { + if ( nodeName( elem, "table" ) && + nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) { + + return jQuery( elem ).children( "tbody" )[ 0 ] || elem; + } + + return elem; +} + +// Replace/restore the type attribute of script elements for safe DOM manipulation +function disableScript( elem ) { + elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type; + return elem; +} +function restoreScript( elem ) { + if ( ( elem.type || "" ).slice( 0, 5 ) === "true/" ) { + elem.type = elem.type.slice( 5 ); + } else { + elem.removeAttribute( "type" ); + } + + return elem; +} + +function cloneCopyEvent( src, dest ) { + var i, l, type, pdataOld, udataOld, udataCur, events; + + if ( dest.nodeType !== 1 ) { + return; + } + + // 1. Copy private data: events, handlers, etc. + if ( dataPriv.hasData( src ) ) { + pdataOld = dataPriv.get( src ); + events = pdataOld.events; + + if ( events ) { + dataPriv.remove( dest, "handle events" ); + + for ( type in events ) { + for ( i = 0, l = events[ type ].length; i < l; i++ ) { + jQuery.event.add( dest, type, events[ type ][ i ] ); + } + } + } + } + + // 2. Copy user data + if ( dataUser.hasData( src ) ) { + udataOld = dataUser.access( src ); + udataCur = jQuery.extend( {}, udataOld ); + + dataUser.set( dest, udataCur ); + } +} + +// Fix IE bugs, see support tests +function fixInput( src, dest ) { + var nodeName = dest.nodeName.toLowerCase(); + + // Fails to persist the checked state of a cloned checkbox or radio button. + if ( nodeName === "input" && rcheckableType.test( src.type ) ) { + dest.checked = src.checked; + + // Fails to return the selected option to the default selected state when cloning options + } else if ( nodeName === "input" || nodeName === "textarea" ) { + dest.defaultValue = src.defaultValue; + } +} + +function domManip( collection, args, callback, ignored ) { + + // Flatten any nested arrays + args = flat( args ); + + var fragment, first, scripts, hasScripts, node, doc, + i = 0, + l = collection.length, + iNoClone = l - 1, + value = args[ 0 ], + valueIsFunction = isFunction( value ); + + // We can't cloneNode fragments that contain checked, in WebKit + if ( valueIsFunction || + ( l > 1 && typeof value === "string" && + !support.checkClone && rchecked.test( value ) ) ) { + return collection.each( function( index ) { + var self = collection.eq( index ); + if ( valueIsFunction ) { + args[ 0 ] = value.call( this, index, self.html() ); + } + domManip( self, args, callback, ignored ); + } ); + } + + if ( l ) { + fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored ); + first = fragment.firstChild; + + if ( fragment.childNodes.length === 1 ) { + fragment = first; + } + + // Require either new content or an interest in ignored elements to invoke the callback + if ( first || ignored ) { + scripts = jQuery.map( getAll( fragment, "script" ), disableScript ); + hasScripts = scripts.length; + + // Use the original fragment for the last item + // instead of the first because it can end up + // being emptied incorrectly in certain situations (#8070). + for ( ; i < l; i++ ) { + node = fragment; + + if ( i !== iNoClone ) { + node = jQuery.clone( node, true, true ); + + // Keep references to cloned scripts for later restoration + if ( hasScripts ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( scripts, getAll( node, "script" ) ); + } + } + + callback.call( collection[ i ], node, i ); + } + + if ( hasScripts ) { + doc = scripts[ scripts.length - 1 ].ownerDocument; + + // Reenable scripts + jQuery.map( scripts, restoreScript ); + + // Evaluate executable scripts on first document insertion + for ( i = 0; i < hasScripts; i++ ) { + node = scripts[ i ]; + if ( rscriptType.test( node.type || "" ) && + !dataPriv.access( node, "globalEval" ) && + jQuery.contains( doc, node ) ) { + + if ( node.src && ( node.type || "" ).toLowerCase() !== "module" ) { + + // Optional AJAX dependency, but won't run scripts if not present + if ( jQuery._evalUrl && !node.noModule ) { + jQuery._evalUrl( node.src, { + nonce: node.nonce || node.getAttribute( "nonce" ) + }, doc ); + } + } else { + DOMEval( node.textContent.replace( rcleanScript, "" ), node, doc ); + } + } + } + } + } + } + + return collection; +} + +function remove( elem, selector, keepData ) { + var node, + nodes = selector ? jQuery.filter( selector, elem ) : elem, + i = 0; + + for ( ; ( node = nodes[ i ] ) != null; i++ ) { + if ( !keepData && node.nodeType === 1 ) { + jQuery.cleanData( getAll( node ) ); + } + + if ( node.parentNode ) { + if ( keepData && isAttached( node ) ) { + setGlobalEval( getAll( node, "script" ) ); + } + node.parentNode.removeChild( node ); + } + } + + return elem; +} + +jQuery.extend( { + htmlPrefilter: function( html ) { + return html; + }, + + clone: function( elem, dataAndEvents, deepDataAndEvents ) { + var i, l, srcElements, destElements, + clone = elem.cloneNode( true ), + inPage = isAttached( elem ); + + // Fix IE cloning issues + if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) && + !jQuery.isXMLDoc( elem ) ) { + + // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2 + destElements = getAll( clone ); + srcElements = getAll( elem ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + fixInput( srcElements[ i ], destElements[ i ] ); + } + } + + // Copy the events from the original to the clone + if ( dataAndEvents ) { + if ( deepDataAndEvents ) { + srcElements = srcElements || getAll( elem ); + destElements = destElements || getAll( clone ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + cloneCopyEvent( srcElements[ i ], destElements[ i ] ); + } + } else { + cloneCopyEvent( elem, clone ); + } + } + + // Preserve script evaluation history + destElements = getAll( clone, "script" ); + if ( destElements.length > 0 ) { + setGlobalEval( destElements, !inPage && getAll( elem, "script" ) ); + } + + // Return the cloned set + return clone; + }, + + cleanData: function( elems ) { + var data, elem, type, + special = jQuery.event.special, + i = 0; + + for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) { + if ( acceptData( elem ) ) { + if ( ( data = elem[ dataPriv.expando ] ) ) { + if ( data.events ) { + for ( type in data.events ) { + if ( special[ type ] ) { + jQuery.event.remove( elem, type ); + + // This is a shortcut to avoid jQuery.event.remove's overhead + } else { + jQuery.removeEvent( elem, type, data.handle ); + } + } + } + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataPriv.expando ] = undefined; + } + if ( elem[ dataUser.expando ] ) { + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataUser.expando ] = undefined; + } + } + } + } +} ); + +jQuery.fn.extend( { + detach: function( selector ) { + return remove( this, selector, true ); + }, + + remove: function( selector ) { + return remove( this, selector ); + }, + + text: function( value ) { + return access( this, function( value ) { + return value === undefined ? + jQuery.text( this ) : + this.empty().each( function() { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + this.textContent = value; + } + } ); + }, null, value, arguments.length ); + }, + + append: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.appendChild( elem ); + } + } ); + }, + + prepend: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.insertBefore( elem, target.firstChild ); + } + } ); + }, + + before: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this ); + } + } ); + }, + + after: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this.nextSibling ); + } + } ); + }, + + empty: function() { + var elem, + i = 0; + + for ( ; ( elem = this[ i ] ) != null; i++ ) { + if ( elem.nodeType === 1 ) { + + // Prevent memory leaks + jQuery.cleanData( getAll( elem, false ) ); + + // Remove any remaining nodes + elem.textContent = ""; + } + } + + return this; + }, + + clone: function( dataAndEvents, deepDataAndEvents ) { + dataAndEvents = dataAndEvents == null ? false : dataAndEvents; + deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; + + return this.map( function() { + return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); + } ); + }, + + html: function( value ) { + return access( this, function( value ) { + var elem = this[ 0 ] || {}, + i = 0, + l = this.length; + + if ( value === undefined && elem.nodeType === 1 ) { + return elem.innerHTML; + } + + // See if we can take a shortcut and just use innerHTML + if ( typeof value === "string" && !rnoInnerhtml.test( value ) && + !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) { + + value = jQuery.htmlPrefilter( value ); + + try { + for ( ; i < l; i++ ) { + elem = this[ i ] || {}; + + // Remove element nodes and prevent memory leaks + if ( elem.nodeType === 1 ) { + jQuery.cleanData( getAll( elem, false ) ); + elem.innerHTML = value; + } + } + + elem = 0; + + // If using innerHTML throws an exception, use the fallback method + } catch ( e ) {} + } + + if ( elem ) { + this.empty().append( value ); + } + }, null, value, arguments.length ); + }, + + replaceWith: function() { + var ignored = []; + + // Make the changes, replacing each non-ignored context element with the new content + return domManip( this, arguments, function( elem ) { + var parent = this.parentNode; + + if ( jQuery.inArray( this, ignored ) < 0 ) { + jQuery.cleanData( getAll( this ) ); + if ( parent ) { + parent.replaceChild( elem, this ); + } + } + + // Force callback invocation + }, ignored ); + } +} ); + +jQuery.each( { + appendTo: "append", + prependTo: "prepend", + insertBefore: "before", + insertAfter: "after", + replaceAll: "replaceWith" +}, function( name, original ) { + jQuery.fn[ name ] = function( selector ) { + var elems, + ret = [], + insert = jQuery( selector ), + last = insert.length - 1, + i = 0; + + for ( ; i <= last; i++ ) { + elems = i === last ? this : this.clone( true ); + jQuery( insert[ i ] )[ original ]( elems ); + + // Support: Android <=4.0 only, PhantomJS 1 only + // .get() because push.apply(_, arraylike) throws on ancient WebKit + push.apply( ret, elems.get() ); + } + + return this.pushStack( ret ); + }; +} ); +var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" ); + +var getStyles = function( elem ) { + + // Support: IE <=11 only, Firefox <=30 (#15098, #14150) + // IE throws on elements created in popups + // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" + var view = elem.ownerDocument.defaultView; + + if ( !view || !view.opener ) { + view = window; + } + + return view.getComputedStyle( elem ); + }; + +var swap = function( elem, options, callback ) { + var ret, name, + old = {}; + + // Remember the old values, and insert the new ones + for ( name in options ) { + old[ name ] = elem.style[ name ]; + elem.style[ name ] = options[ name ]; + } + + ret = callback.call( elem ); + + // Revert the old values + for ( name in options ) { + elem.style[ name ] = old[ name ]; + } + + return ret; +}; + + +var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" ); + + + +( function() { + + // Executing both pixelPosition & boxSizingReliable tests require only one layout + // so they're executed at the same time to save the second computation. + function computeStyleTests() { + + // This is a singleton, we need to execute it only once + if ( !div ) { + return; + } + + container.style.cssText = "position:absolute;left:-11111px;width:60px;" + + "margin-top:1px;padding:0;border:0"; + div.style.cssText = + "position:relative;display:block;box-sizing:border-box;overflow:scroll;" + + "margin:auto;border:1px;padding:1px;" + + "width:60%;top:1%"; + documentElement.appendChild( container ).appendChild( div ); + + var divStyle = window.getComputedStyle( div ); + pixelPositionVal = divStyle.top !== "1%"; + + // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44 + reliableMarginLeftVal = roundPixelMeasures( divStyle.marginLeft ) === 12; + + // Support: Android 4.0 - 4.3 only, Safari <=9.1 - 10.1, iOS <=7.0 - 9.3 + // Some styles come back with percentage values, even though they shouldn't + div.style.right = "60%"; + pixelBoxStylesVal = roundPixelMeasures( divStyle.right ) === 36; + + // Support: IE 9 - 11 only + // Detect misreporting of content dimensions for box-sizing:border-box elements + boxSizingReliableVal = roundPixelMeasures( divStyle.width ) === 36; + + // Support: IE 9 only + // Detect overflow:scroll screwiness (gh-3699) + // Support: Chrome <=64 + // Don't get tricked when zoom affects offsetWidth (gh-4029) + div.style.position = "absolute"; + scrollboxSizeVal = roundPixelMeasures( div.offsetWidth / 3 ) === 12; + + documentElement.removeChild( container ); + + // Nullify the div so it wouldn't be stored in the memory and + // it will also be a sign that checks already performed + div = null; + } + + function roundPixelMeasures( measure ) { + return Math.round( parseFloat( measure ) ); + } + + var pixelPositionVal, boxSizingReliableVal, scrollboxSizeVal, pixelBoxStylesVal, + reliableTrDimensionsVal, reliableMarginLeftVal, + container = document.createElement( "div" ), + div = document.createElement( "div" ); + + // Finish early in limited (non-browser) environments + if ( !div.style ) { + return; + } + + // Support: IE <=9 - 11 only + // Style of cloned element affects source element cloned (#8908) + div.style.backgroundClip = "content-box"; + div.cloneNode( true ).style.backgroundClip = ""; + support.clearCloneStyle = div.style.backgroundClip === "content-box"; + + jQuery.extend( support, { + boxSizingReliable: function() { + computeStyleTests(); + return boxSizingReliableVal; + }, + pixelBoxStyles: function() { + computeStyleTests(); + return pixelBoxStylesVal; + }, + pixelPosition: function() { + computeStyleTests(); + return pixelPositionVal; + }, + reliableMarginLeft: function() { + computeStyleTests(); + return reliableMarginLeftVal; + }, + scrollboxSize: function() { + computeStyleTests(); + return scrollboxSizeVal; + }, + + // Support: IE 9 - 11+, Edge 15 - 18+ + // IE/Edge misreport `getComputedStyle` of table rows with width/height + // set in CSS while `offset*` properties report correct values. + // Behavior in IE 9 is more subtle than in newer versions & it passes + // some versions of this test; make sure not to make it pass there! + reliableTrDimensions: function() { + var table, tr, trChild, trStyle; + if ( reliableTrDimensionsVal == null ) { + table = document.createElement( "table" ); + tr = document.createElement( "tr" ); + trChild = document.createElement( "div" ); + + table.style.cssText = "position:absolute;left:-11111px"; + tr.style.height = "1px"; + trChild.style.height = "9px"; + + documentElement + .appendChild( table ) + .appendChild( tr ) + .appendChild( trChild ); + + trStyle = window.getComputedStyle( tr ); + reliableTrDimensionsVal = parseInt( trStyle.height ) > 3; + + documentElement.removeChild( table ); + } + return reliableTrDimensionsVal; + } + } ); +} )(); + + +function curCSS( elem, name, computed ) { + var width, minWidth, maxWidth, ret, + + // Support: Firefox 51+ + // Retrieving style before computed somehow + // fixes an issue with getting wrong values + // on detached elements + style = elem.style; + + computed = computed || getStyles( elem ); + + // getPropertyValue is needed for: + // .css('filter') (IE 9 only, #12537) + // .css('--customProperty) (#3144) + if ( computed ) { + ret = computed.getPropertyValue( name ) || computed[ name ]; + + if ( ret === "" && !isAttached( elem ) ) { + ret = jQuery.style( elem, name ); + } + + // A tribute to the "awesome hack by Dean Edwards" + // Android Browser returns percentage for some values, + // but width seems to be reliably pixels. + // This is against the CSSOM draft spec: + // https://drafts.csswg.org/cssom/#resolved-values + if ( !support.pixelBoxStyles() && rnumnonpx.test( ret ) && rboxStyle.test( name ) ) { + + // Remember the original values + width = style.width; + minWidth = style.minWidth; + maxWidth = style.maxWidth; + + // Put in the new values to get a computed value out + style.minWidth = style.maxWidth = style.width = ret; + ret = computed.width; + + // Revert the changed values + style.width = width; + style.minWidth = minWidth; + style.maxWidth = maxWidth; + } + } + + return ret !== undefined ? + + // Support: IE <=9 - 11 only + // IE returns zIndex value as an integer. + ret + "" : + ret; +} + + +function addGetHookIf( conditionFn, hookFn ) { + + // Define the hook, we'll check on the first run if it's really needed. + return { + get: function() { + if ( conditionFn() ) { + + // Hook not needed (or it's not possible to use it due + // to missing dependency), remove it. + delete this.get; + return; + } + + // Hook needed; redefine it so that the support test is not executed again. + return ( this.get = hookFn ).apply( this, arguments ); + } + }; +} + + +var cssPrefixes = [ "Webkit", "Moz", "ms" ], + emptyStyle = document.createElement( "div" ).style, + vendorProps = {}; + +// Return a vendor-prefixed property or undefined +function vendorPropName( name ) { + + // Check for vendor prefixed names + var capName = name[ 0 ].toUpperCase() + name.slice( 1 ), + i = cssPrefixes.length; + + while ( i-- ) { + name = cssPrefixes[ i ] + capName; + if ( name in emptyStyle ) { + return name; + } + } +} + +// Return a potentially-mapped jQuery.cssProps or vendor prefixed property +function finalPropName( name ) { + var final = jQuery.cssProps[ name ] || vendorProps[ name ]; + + if ( final ) { + return final; + } + if ( name in emptyStyle ) { + return name; + } + return vendorProps[ name ] = vendorPropName( name ) || name; +} + + +var + + // Swappable if display is none or starts with table + // except "table", "table-cell", or "table-caption" + // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display + rdisplayswap = /^(none|table(?!-c[ea]).+)/, + rcustomProp = /^--/, + cssShow = { position: "absolute", visibility: "hidden", display: "block" }, + cssNormalTransform = { + letterSpacing: "0", + fontWeight: "400" + }; + +function setPositiveNumber( _elem, value, subtract ) { + + // Any relative (+/-) values have already been + // normalized at this point + var matches = rcssNum.exec( value ); + return matches ? + + // Guard against undefined "subtract", e.g., when used as in cssHooks + Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) : + value; +} + +function boxModelAdjustment( elem, dimension, box, isBorderBox, styles, computedVal ) { + var i = dimension === "width" ? 1 : 0, + extra = 0, + delta = 0; + + // Adjustment may not be necessary + if ( box === ( isBorderBox ? "border" : "content" ) ) { + return 0; + } + + for ( ; i < 4; i += 2 ) { + + // Both box models exclude margin + if ( box === "margin" ) { + delta += jQuery.css( elem, box + cssExpand[ i ], true, styles ); + } + + // If we get here with a content-box, we're seeking "padding" or "border" or "margin" + if ( !isBorderBox ) { + + // Add padding + delta += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + + // For "border" or "margin", add border + if ( box !== "padding" ) { + delta += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + + // But still keep track of it otherwise + } else { + extra += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + + // If we get here with a border-box (content + padding + border), we're seeking "content" or + // "padding" or "margin" + } else { + + // For "content", subtract padding + if ( box === "content" ) { + delta -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + } + + // For "content" or "padding", subtract border + if ( box !== "margin" ) { + delta -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + } + } + + // Account for positive content-box scroll gutter when requested by providing computedVal + if ( !isBorderBox && computedVal >= 0 ) { + + // offsetWidth/offsetHeight is a rounded sum of content, padding, scroll gutter, and border + // Assuming integer scroll gutter, subtract the rest and round down + delta += Math.max( 0, Math.ceil( + elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - + computedVal - + delta - + extra - + 0.5 + + // If offsetWidth/offsetHeight is unknown, then we can't determine content-box scroll gutter + // Use an explicit zero to avoid NaN (gh-3964) + ) ) || 0; + } + + return delta; +} + +function getWidthOrHeight( elem, dimension, extra ) { + + // Start with computed style + var styles = getStyles( elem ), + + // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-4322). + // Fake content-box until we know it's needed to know the true value. + boxSizingNeeded = !support.boxSizingReliable() || extra, + isBorderBox = boxSizingNeeded && + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + valueIsBorderBox = isBorderBox, + + val = curCSS( elem, dimension, styles ), + offsetProp = "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ); + + // Support: Firefox <=54 + // Return a confounding non-pixel value or feign ignorance, as appropriate. + if ( rnumnonpx.test( val ) ) { + if ( !extra ) { + return val; + } + val = "auto"; + } + + + // Support: IE 9 - 11 only + // Use offsetWidth/offsetHeight for when box sizing is unreliable. + // In those cases, the computed value can be trusted to be border-box. + if ( ( !support.boxSizingReliable() && isBorderBox || + + // Support: IE 10 - 11+, Edge 15 - 18+ + // IE/Edge misreport `getComputedStyle` of table rows with width/height + // set in CSS while `offset*` properties report correct values. + // Interestingly, in some cases IE 9 doesn't suffer from this issue. + !support.reliableTrDimensions() && nodeName( elem, "tr" ) || + + // Fall back to offsetWidth/offsetHeight when value is "auto" + // This happens for inline elements with no explicit setting (gh-3571) + val === "auto" || + + // Support: Android <=4.1 - 4.3 only + // Also use offsetWidth/offsetHeight for misreported inline dimensions (gh-3602) + !parseFloat( val ) && jQuery.css( elem, "display", false, styles ) === "inline" ) && + + // Make sure the element is visible & connected + elem.getClientRects().length ) { + + isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box"; + + // Where available, offsetWidth/offsetHeight approximate border box dimensions. + // Where not available (e.g., SVG), assume unreliable box-sizing and interpret the + // retrieved value as a content box dimension. + valueIsBorderBox = offsetProp in elem; + if ( valueIsBorderBox ) { + val = elem[ offsetProp ]; + } + } + + // Normalize "" and auto + val = parseFloat( val ) || 0; + + // Adjust for the element's box model + return ( val + + boxModelAdjustment( + elem, + dimension, + extra || ( isBorderBox ? "border" : "content" ), + valueIsBorderBox, + styles, + + // Provide the current computed size to request scroll gutter calculation (gh-3589) + val + ) + ) + "px"; +} + +jQuery.extend( { + + // Add in style property hooks for overriding the default + // behavior of getting and setting a style property + cssHooks: { + opacity: { + get: function( elem, computed ) { + if ( computed ) { + + // We should always get a number back from opacity + var ret = curCSS( elem, "opacity" ); + return ret === "" ? "1" : ret; + } + } + } + }, + + // Don't automatically add "px" to these possibly-unitless properties + cssNumber: { + "animationIterationCount": true, + "columnCount": true, + "fillOpacity": true, + "flexGrow": true, + "flexShrink": true, + "fontWeight": true, + "gridArea": true, + "gridColumn": true, + "gridColumnEnd": true, + "gridColumnStart": true, + "gridRow": true, + "gridRowEnd": true, + "gridRowStart": true, + "lineHeight": true, + "opacity": true, + "order": true, + "orphans": true, + "widows": true, + "zIndex": true, + "zoom": true + }, + + // Add in properties whose names you wish to fix before + // setting or getting the value + cssProps: {}, + + // Get and set the style property on a DOM Node + style: function( elem, name, value, extra ) { + + // Don't set styles on text and comment nodes + if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) { + return; + } + + // Make sure that we're working with the right name + var ret, type, hooks, + origName = camelCase( name ), + isCustomProp = rcustomProp.test( name ), + style = elem.style; + + // Make sure that we're working with the right name. We don't + // want to query the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Gets hook for the prefixed version, then unprefixed version + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // Check if we're setting a value + if ( value !== undefined ) { + type = typeof value; + + // Convert "+=" or "-=" to relative numbers (#7345) + if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) { + value = adjustCSS( elem, name, ret ); + + // Fixes bug #9237 + type = "number"; + } + + // Make sure that null and NaN values aren't set (#7116) + if ( value == null || value !== value ) { + return; + } + + // If a number was passed in, add the unit (except for certain CSS properties) + // The isCustomProp check can be removed in jQuery 4.0 when we only auto-append + // "px" to a few hardcoded values. + if ( type === "number" && !isCustomProp ) { + value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" ); + } + + // background-* props affect original clone's values + if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) { + style[ name ] = "inherit"; + } + + // If a hook was provided, use that value, otherwise just set the specified value + if ( !hooks || !( "set" in hooks ) || + ( value = hooks.set( elem, value, extra ) ) !== undefined ) { + + if ( isCustomProp ) { + style.setProperty( name, value ); + } else { + style[ name ] = value; + } + } + + } else { + + // If a hook was provided get the non-computed value from there + if ( hooks && "get" in hooks && + ( ret = hooks.get( elem, false, extra ) ) !== undefined ) { + + return ret; + } + + // Otherwise just get the value from the style object + return style[ name ]; + } + }, + + css: function( elem, name, extra, styles ) { + var val, num, hooks, + origName = camelCase( name ), + isCustomProp = rcustomProp.test( name ); + + // Make sure that we're working with the right name. We don't + // want to modify the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Try prefixed name followed by the unprefixed name + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // If a hook was provided get the computed value from there + if ( hooks && "get" in hooks ) { + val = hooks.get( elem, true, extra ); + } + + // Otherwise, if a way to get the computed value exists, use that + if ( val === undefined ) { + val = curCSS( elem, name, styles ); + } + + // Convert "normal" to computed value + if ( val === "normal" && name in cssNormalTransform ) { + val = cssNormalTransform[ name ]; + } + + // Make numeric if forced or a qualifier was provided and val looks numeric + if ( extra === "" || extra ) { + num = parseFloat( val ); + return extra === true || isFinite( num ) ? num || 0 : val; + } + + return val; + } +} ); + +jQuery.each( [ "height", "width" ], function( _i, dimension ) { + jQuery.cssHooks[ dimension ] = { + get: function( elem, computed, extra ) { + if ( computed ) { + + // Certain elements can have dimension info if we invisibly show them + // but it must have a current display style that would benefit + return rdisplayswap.test( jQuery.css( elem, "display" ) ) && + + // Support: Safari 8+ + // Table columns in Safari have non-zero offsetWidth & zero + // getBoundingClientRect().width unless display is changed. + // Support: IE <=11 only + // Running getBoundingClientRect on a disconnected node + // in IE throws an error. + ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ? + swap( elem, cssShow, function() { + return getWidthOrHeight( elem, dimension, extra ); + } ) : + getWidthOrHeight( elem, dimension, extra ); + } + }, + + set: function( elem, value, extra ) { + var matches, + styles = getStyles( elem ), + + // Only read styles.position if the test has a chance to fail + // to avoid forcing a reflow. + scrollboxSizeBuggy = !support.scrollboxSize() && + styles.position === "absolute", + + // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-3991) + boxSizingNeeded = scrollboxSizeBuggy || extra, + isBorderBox = boxSizingNeeded && + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + subtract = extra ? + boxModelAdjustment( + elem, + dimension, + extra, + isBorderBox, + styles + ) : + 0; + + // Account for unreliable border-box dimensions by comparing offset* to computed and + // faking a content-box to get border and padding (gh-3699) + if ( isBorderBox && scrollboxSizeBuggy ) { + subtract -= Math.ceil( + elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - + parseFloat( styles[ dimension ] ) - + boxModelAdjustment( elem, dimension, "border", false, styles ) - + 0.5 + ); + } + + // Convert to pixels if value adjustment is needed + if ( subtract && ( matches = rcssNum.exec( value ) ) && + ( matches[ 3 ] || "px" ) !== "px" ) { + + elem.style[ dimension ] = value; + value = jQuery.css( elem, dimension ); + } + + return setPositiveNumber( elem, value, subtract ); + } + }; +} ); + +jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft, + function( elem, computed ) { + if ( computed ) { + return ( parseFloat( curCSS( elem, "marginLeft" ) ) || + elem.getBoundingClientRect().left - + swap( elem, { marginLeft: 0 }, function() { + return elem.getBoundingClientRect().left; + } ) + ) + "px"; + } + } +); + +// These hooks are used by animate to expand properties +jQuery.each( { + margin: "", + padding: "", + border: "Width" +}, function( prefix, suffix ) { + jQuery.cssHooks[ prefix + suffix ] = { + expand: function( value ) { + var i = 0, + expanded = {}, + + // Assumes a single number if not a string + parts = typeof value === "string" ? value.split( " " ) : [ value ]; + + for ( ; i < 4; i++ ) { + expanded[ prefix + cssExpand[ i ] + suffix ] = + parts[ i ] || parts[ i - 2 ] || parts[ 0 ]; + } + + return expanded; + } + }; + + if ( prefix !== "margin" ) { + jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber; + } +} ); + +jQuery.fn.extend( { + css: function( name, value ) { + return access( this, function( elem, name, value ) { + var styles, len, + map = {}, + i = 0; + + if ( Array.isArray( name ) ) { + styles = getStyles( elem ); + len = name.length; + + for ( ; i < len; i++ ) { + map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles ); + } + + return map; + } + + return value !== undefined ? + jQuery.style( elem, name, value ) : + jQuery.css( elem, name ); + }, name, value, arguments.length > 1 ); + } +} ); + + +function Tween( elem, options, prop, end, easing ) { + return new Tween.prototype.init( elem, options, prop, end, easing ); +} +jQuery.Tween = Tween; + +Tween.prototype = { + constructor: Tween, + init: function( elem, options, prop, end, easing, unit ) { + this.elem = elem; + this.prop = prop; + this.easing = easing || jQuery.easing._default; + this.options = options; + this.start = this.now = this.cur(); + this.end = end; + this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" ); + }, + cur: function() { + var hooks = Tween.propHooks[ this.prop ]; + + return hooks && hooks.get ? + hooks.get( this ) : + Tween.propHooks._default.get( this ); + }, + run: function( percent ) { + var eased, + hooks = Tween.propHooks[ this.prop ]; + + if ( this.options.duration ) { + this.pos = eased = jQuery.easing[ this.easing ]( + percent, this.options.duration * percent, 0, 1, this.options.duration + ); + } else { + this.pos = eased = percent; + } + this.now = ( this.end - this.start ) * eased + this.start; + + if ( this.options.step ) { + this.options.step.call( this.elem, this.now, this ); + } + + if ( hooks && hooks.set ) { + hooks.set( this ); + } else { + Tween.propHooks._default.set( this ); + } + return this; + } +}; + +Tween.prototype.init.prototype = Tween.prototype; + +Tween.propHooks = { + _default: { + get: function( tween ) { + var result; + + // Use a property on the element directly when it is not a DOM element, + // or when there is no matching style property that exists. + if ( tween.elem.nodeType !== 1 || + tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) { + return tween.elem[ tween.prop ]; + } + + // Passing an empty string as a 3rd parameter to .css will automatically + // attempt a parseFloat and fallback to a string if the parse fails. + // Simple values such as "10px" are parsed to Float; + // complex values such as "rotate(1rad)" are returned as-is. + result = jQuery.css( tween.elem, tween.prop, "" ); + + // Empty strings, null, undefined and "auto" are converted to 0. + return !result || result === "auto" ? 0 : result; + }, + set: function( tween ) { + + // Use step hook for back compat. + // Use cssHook if its there. + // Use .style if available and use plain properties where available. + if ( jQuery.fx.step[ tween.prop ] ) { + jQuery.fx.step[ tween.prop ]( tween ); + } else if ( tween.elem.nodeType === 1 && ( + jQuery.cssHooks[ tween.prop ] || + tween.elem.style[ finalPropName( tween.prop ) ] != null ) ) { + jQuery.style( tween.elem, tween.prop, tween.now + tween.unit ); + } else { + tween.elem[ tween.prop ] = tween.now; + } + } + } +}; + +// Support: IE <=9 only +// Panic based approach to setting things on disconnected nodes +Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = { + set: function( tween ) { + if ( tween.elem.nodeType && tween.elem.parentNode ) { + tween.elem[ tween.prop ] = tween.now; + } + } +}; + +jQuery.easing = { + linear: function( p ) { + return p; + }, + swing: function( p ) { + return 0.5 - Math.cos( p * Math.PI ) / 2; + }, + _default: "swing" +}; + +jQuery.fx = Tween.prototype.init; + +// Back compat <1.8 extension point +jQuery.fx.step = {}; + + + + +var + fxNow, inProgress, + rfxtypes = /^(?:toggle|show|hide)$/, + rrun = /queueHooks$/; + +function schedule() { + if ( inProgress ) { + if ( document.hidden === false && window.requestAnimationFrame ) { + window.requestAnimationFrame( schedule ); + } else { + window.setTimeout( schedule, jQuery.fx.interval ); + } + + jQuery.fx.tick(); + } +} + +// Animations created synchronously will run synchronously +function createFxNow() { + window.setTimeout( function() { + fxNow = undefined; + } ); + return ( fxNow = Date.now() ); +} + +// Generate parameters to create a standard animation +function genFx( type, includeWidth ) { + var which, + i = 0, + attrs = { height: type }; + + // If we include width, step value is 1 to do all cssExpand values, + // otherwise step value is 2 to skip over Left and Right + includeWidth = includeWidth ? 1 : 0; + for ( ; i < 4; i += 2 - includeWidth ) { + which = cssExpand[ i ]; + attrs[ "margin" + which ] = attrs[ "padding" + which ] = type; + } + + if ( includeWidth ) { + attrs.opacity = attrs.width = type; + } + + return attrs; +} + +function createTween( value, prop, animation ) { + var tween, + collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ), + index = 0, + length = collection.length; + for ( ; index < length; index++ ) { + if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) { + + // We're done with this property + return tween; + } + } +} + +function defaultPrefilter( elem, props, opts ) { + var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display, + isBox = "width" in props || "height" in props, + anim = this, + orig = {}, + style = elem.style, + hidden = elem.nodeType && isHiddenWithinTree( elem ), + dataShow = dataPriv.get( elem, "fxshow" ); + + // Queue-skipping animations hijack the fx hooks + if ( !opts.queue ) { + hooks = jQuery._queueHooks( elem, "fx" ); + if ( hooks.unqueued == null ) { + hooks.unqueued = 0; + oldfire = hooks.empty.fire; + hooks.empty.fire = function() { + if ( !hooks.unqueued ) { + oldfire(); + } + }; + } + hooks.unqueued++; + + anim.always( function() { + + // Ensure the complete handler is called before this completes + anim.always( function() { + hooks.unqueued--; + if ( !jQuery.queue( elem, "fx" ).length ) { + hooks.empty.fire(); + } + } ); + } ); + } + + // Detect show/hide animations + for ( prop in props ) { + value = props[ prop ]; + if ( rfxtypes.test( value ) ) { + delete props[ prop ]; + toggle = toggle || value === "toggle"; + if ( value === ( hidden ? "hide" : "show" ) ) { + + // Pretend to be hidden if this is a "show" and + // there is still data from a stopped show/hide + if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) { + hidden = true; + + // Ignore all other no-op show/hide data + } else { + continue; + } + } + orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop ); + } + } + + // Bail out if this is a no-op like .hide().hide() + propTween = !jQuery.isEmptyObject( props ); + if ( !propTween && jQuery.isEmptyObject( orig ) ) { + return; + } + + // Restrict "overflow" and "display" styles during box animations + if ( isBox && elem.nodeType === 1 ) { + + // Support: IE <=9 - 11, Edge 12 - 15 + // Record all 3 overflow attributes because IE does not infer the shorthand + // from identically-valued overflowX and overflowY and Edge just mirrors + // the overflowX value there. + opts.overflow = [ style.overflow, style.overflowX, style.overflowY ]; + + // Identify a display type, preferring old show/hide data over the CSS cascade + restoreDisplay = dataShow && dataShow.display; + if ( restoreDisplay == null ) { + restoreDisplay = dataPriv.get( elem, "display" ); + } + display = jQuery.css( elem, "display" ); + if ( display === "none" ) { + if ( restoreDisplay ) { + display = restoreDisplay; + } else { + + // Get nonempty value(s) by temporarily forcing visibility + showHide( [ elem ], true ); + restoreDisplay = elem.style.display || restoreDisplay; + display = jQuery.css( elem, "display" ); + showHide( [ elem ] ); + } + } + + // Animate inline elements as inline-block + if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) { + if ( jQuery.css( elem, "float" ) === "none" ) { + + // Restore the original display value at the end of pure show/hide animations + if ( !propTween ) { + anim.done( function() { + style.display = restoreDisplay; + } ); + if ( restoreDisplay == null ) { + display = style.display; + restoreDisplay = display === "none" ? "" : display; + } + } + style.display = "inline-block"; + } + } + } + + if ( opts.overflow ) { + style.overflow = "hidden"; + anim.always( function() { + style.overflow = opts.overflow[ 0 ]; + style.overflowX = opts.overflow[ 1 ]; + style.overflowY = opts.overflow[ 2 ]; + } ); + } + + // Implement show/hide animations + propTween = false; + for ( prop in orig ) { + + // General show/hide setup for this element animation + if ( !propTween ) { + if ( dataShow ) { + if ( "hidden" in dataShow ) { + hidden = dataShow.hidden; + } + } else { + dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } ); + } + + // Store hidden/visible for toggle so `.stop().toggle()` "reverses" + if ( toggle ) { + dataShow.hidden = !hidden; + } + + // Show elements before animating them + if ( hidden ) { + showHide( [ elem ], true ); + } + + /* eslint-disable no-loop-func */ + + anim.done( function() { + + /* eslint-enable no-loop-func */ + + // The final step of a "hide" animation is actually hiding the element + if ( !hidden ) { + showHide( [ elem ] ); + } + dataPriv.remove( elem, "fxshow" ); + for ( prop in orig ) { + jQuery.style( elem, prop, orig[ prop ] ); + } + } ); + } + + // Per-property setup + propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim ); + if ( !( prop in dataShow ) ) { + dataShow[ prop ] = propTween.start; + if ( hidden ) { + propTween.end = propTween.start; + propTween.start = 0; + } + } + } +} + +function propFilter( props, specialEasing ) { + var index, name, easing, value, hooks; + + // camelCase, specialEasing and expand cssHook pass + for ( index in props ) { + name = camelCase( index ); + easing = specialEasing[ name ]; + value = props[ index ]; + if ( Array.isArray( value ) ) { + easing = value[ 1 ]; + value = props[ index ] = value[ 0 ]; + } + + if ( index !== name ) { + props[ name ] = value; + delete props[ index ]; + } + + hooks = jQuery.cssHooks[ name ]; + if ( hooks && "expand" in hooks ) { + value = hooks.expand( value ); + delete props[ name ]; + + // Not quite $.extend, this won't overwrite existing keys. + // Reusing 'index' because we have the correct "name" + for ( index in value ) { + if ( !( index in props ) ) { + props[ index ] = value[ index ]; + specialEasing[ index ] = easing; + } + } + } else { + specialEasing[ name ] = easing; + } + } +} + +function Animation( elem, properties, options ) { + var result, + stopped, + index = 0, + length = Animation.prefilters.length, + deferred = jQuery.Deferred().always( function() { + + // Don't match elem in the :animated selector + delete tick.elem; + } ), + tick = function() { + if ( stopped ) { + return false; + } + var currentTime = fxNow || createFxNow(), + remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ), + + // Support: Android 2.3 only + // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497) + temp = remaining / animation.duration || 0, + percent = 1 - temp, + index = 0, + length = animation.tweens.length; + + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( percent ); + } + + deferred.notifyWith( elem, [ animation, percent, remaining ] ); + + // If there's more to do, yield + if ( percent < 1 && length ) { + return remaining; + } + + // If this was an empty animation, synthesize a final progress notification + if ( !length ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + } + + // Resolve the animation and report its conclusion + deferred.resolveWith( elem, [ animation ] ); + return false; + }, + animation = deferred.promise( { + elem: elem, + props: jQuery.extend( {}, properties ), + opts: jQuery.extend( true, { + specialEasing: {}, + easing: jQuery.easing._default + }, options ), + originalProperties: properties, + originalOptions: options, + startTime: fxNow || createFxNow(), + duration: options.duration, + tweens: [], + createTween: function( prop, end ) { + var tween = jQuery.Tween( elem, animation.opts, prop, end, + animation.opts.specialEasing[ prop ] || animation.opts.easing ); + animation.tweens.push( tween ); + return tween; + }, + stop: function( gotoEnd ) { + var index = 0, + + // If we are going to the end, we want to run all the tweens + // otherwise we skip this part + length = gotoEnd ? animation.tweens.length : 0; + if ( stopped ) { + return this; + } + stopped = true; + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( 1 ); + } + + // Resolve when we played the last frame; otherwise, reject + if ( gotoEnd ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + deferred.resolveWith( elem, [ animation, gotoEnd ] ); + } else { + deferred.rejectWith( elem, [ animation, gotoEnd ] ); + } + return this; + } + } ), + props = animation.props; + + propFilter( props, animation.opts.specialEasing ); + + for ( ; index < length; index++ ) { + result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts ); + if ( result ) { + if ( isFunction( result.stop ) ) { + jQuery._queueHooks( animation.elem, animation.opts.queue ).stop = + result.stop.bind( result ); + } + return result; + } + } + + jQuery.map( props, createTween, animation ); + + if ( isFunction( animation.opts.start ) ) { + animation.opts.start.call( elem, animation ); + } + + // Attach callbacks from options + animation + .progress( animation.opts.progress ) + .done( animation.opts.done, animation.opts.complete ) + .fail( animation.opts.fail ) + .always( animation.opts.always ); + + jQuery.fx.timer( + jQuery.extend( tick, { + elem: elem, + anim: animation, + queue: animation.opts.queue + } ) + ); + + return animation; +} + +jQuery.Animation = jQuery.extend( Animation, { + + tweeners: { + "*": [ function( prop, value ) { + var tween = this.createTween( prop, value ); + adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween ); + return tween; + } ] + }, + + tweener: function( props, callback ) { + if ( isFunction( props ) ) { + callback = props; + props = [ "*" ]; + } else { + props = props.match( rnothtmlwhite ); + } + + var prop, + index = 0, + length = props.length; + + for ( ; index < length; index++ ) { + prop = props[ index ]; + Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || []; + Animation.tweeners[ prop ].unshift( callback ); + } + }, + + prefilters: [ defaultPrefilter ], + + prefilter: function( callback, prepend ) { + if ( prepend ) { + Animation.prefilters.unshift( callback ); + } else { + Animation.prefilters.push( callback ); + } + } +} ); + +jQuery.speed = function( speed, easing, fn ) { + var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : { + complete: fn || !fn && easing || + isFunction( speed ) && speed, + duration: speed, + easing: fn && easing || easing && !isFunction( easing ) && easing + }; + + // Go to the end state if fx are off + if ( jQuery.fx.off ) { + opt.duration = 0; + + } else { + if ( typeof opt.duration !== "number" ) { + if ( opt.duration in jQuery.fx.speeds ) { + opt.duration = jQuery.fx.speeds[ opt.duration ]; + + } else { + opt.duration = jQuery.fx.speeds._default; + } + } + } + + // Normalize opt.queue - true/undefined/null -> "fx" + if ( opt.queue == null || opt.queue === true ) { + opt.queue = "fx"; + } + + // Queueing + opt.old = opt.complete; + + opt.complete = function() { + if ( isFunction( opt.old ) ) { + opt.old.call( this ); + } + + if ( opt.queue ) { + jQuery.dequeue( this, opt.queue ); + } + }; + + return opt; +}; + +jQuery.fn.extend( { + fadeTo: function( speed, to, easing, callback ) { + + // Show any hidden elements after setting opacity to 0 + return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show() + + // Animate to the value specified + .end().animate( { opacity: to }, speed, easing, callback ); + }, + animate: function( prop, speed, easing, callback ) { + var empty = jQuery.isEmptyObject( prop ), + optall = jQuery.speed( speed, easing, callback ), + doAnimation = function() { + + // Operate on a copy of prop so per-property easing won't be lost + var anim = Animation( this, jQuery.extend( {}, prop ), optall ); + + // Empty animations, or finishing resolves immediately + if ( empty || dataPriv.get( this, "finish" ) ) { + anim.stop( true ); + } + }; + doAnimation.finish = doAnimation; + + return empty || optall.queue === false ? + this.each( doAnimation ) : + this.queue( optall.queue, doAnimation ); + }, + stop: function( type, clearQueue, gotoEnd ) { + var stopQueue = function( hooks ) { + var stop = hooks.stop; + delete hooks.stop; + stop( gotoEnd ); + }; + + if ( typeof type !== "string" ) { + gotoEnd = clearQueue; + clearQueue = type; + type = undefined; + } + if ( clearQueue ) { + this.queue( type || "fx", [] ); + } + + return this.each( function() { + var dequeue = true, + index = type != null && type + "queueHooks", + timers = jQuery.timers, + data = dataPriv.get( this ); + + if ( index ) { + if ( data[ index ] && data[ index ].stop ) { + stopQueue( data[ index ] ); + } + } else { + for ( index in data ) { + if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) { + stopQueue( data[ index ] ); + } + } + } + + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && + ( type == null || timers[ index ].queue === type ) ) { + + timers[ index ].anim.stop( gotoEnd ); + dequeue = false; + timers.splice( index, 1 ); + } + } + + // Start the next in the queue if the last step wasn't forced. + // Timers currently will call their complete callbacks, which + // will dequeue but only if they were gotoEnd. + if ( dequeue || !gotoEnd ) { + jQuery.dequeue( this, type ); + } + } ); + }, + finish: function( type ) { + if ( type !== false ) { + type = type || "fx"; + } + return this.each( function() { + var index, + data = dataPriv.get( this ), + queue = data[ type + "queue" ], + hooks = data[ type + "queueHooks" ], + timers = jQuery.timers, + length = queue ? queue.length : 0; + + // Enable finishing flag on private data + data.finish = true; + + // Empty the queue first + jQuery.queue( this, type, [] ); + + if ( hooks && hooks.stop ) { + hooks.stop.call( this, true ); + } + + // Look for any active animations, and finish them + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && timers[ index ].queue === type ) { + timers[ index ].anim.stop( true ); + timers.splice( index, 1 ); + } + } + + // Look for any animations in the old queue and finish them + for ( index = 0; index < length; index++ ) { + if ( queue[ index ] && queue[ index ].finish ) { + queue[ index ].finish.call( this ); + } + } + + // Turn off finishing flag + delete data.finish; + } ); + } +} ); + +jQuery.each( [ "toggle", "show", "hide" ], function( _i, name ) { + var cssFn = jQuery.fn[ name ]; + jQuery.fn[ name ] = function( speed, easing, callback ) { + return speed == null || typeof speed === "boolean" ? + cssFn.apply( this, arguments ) : + this.animate( genFx( name, true ), speed, easing, callback ); + }; +} ); + +// Generate shortcuts for custom animations +jQuery.each( { + slideDown: genFx( "show" ), + slideUp: genFx( "hide" ), + slideToggle: genFx( "toggle" ), + fadeIn: { opacity: "show" }, + fadeOut: { opacity: "hide" }, + fadeToggle: { opacity: "toggle" } +}, function( name, props ) { + jQuery.fn[ name ] = function( speed, easing, callback ) { + return this.animate( props, speed, easing, callback ); + }; +} ); + +jQuery.timers = []; +jQuery.fx.tick = function() { + var timer, + i = 0, + timers = jQuery.timers; + + fxNow = Date.now(); + + for ( ; i < timers.length; i++ ) { + timer = timers[ i ]; + + // Run the timer and safely remove it when done (allowing for external removal) + if ( !timer() && timers[ i ] === timer ) { + timers.splice( i--, 1 ); + } + } + + if ( !timers.length ) { + jQuery.fx.stop(); + } + fxNow = undefined; +}; + +jQuery.fx.timer = function( timer ) { + jQuery.timers.push( timer ); + jQuery.fx.start(); +}; + +jQuery.fx.interval = 13; +jQuery.fx.start = function() { + if ( inProgress ) { + return; + } + + inProgress = true; + schedule(); +}; + +jQuery.fx.stop = function() { + inProgress = null; +}; + +jQuery.fx.speeds = { + slow: 600, + fast: 200, + + // Default speed + _default: 400 +}; + + +// Based off of the plugin by Clint Helfers, with permission. +// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/ +jQuery.fn.delay = function( time, type ) { + time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; + type = type || "fx"; + + return this.queue( type, function( next, hooks ) { + var timeout = window.setTimeout( next, time ); + hooks.stop = function() { + window.clearTimeout( timeout ); + }; + } ); +}; + + +( function() { + var input = document.createElement( "input" ), + select = document.createElement( "select" ), + opt = select.appendChild( document.createElement( "option" ) ); + + input.type = "checkbox"; + + // Support: Android <=4.3 only + // Default value for a checkbox should be "on" + support.checkOn = input.value !== ""; + + // Support: IE <=11 only + // Must access selectedIndex to make default options select + support.optSelected = opt.selected; + + // Support: IE <=11 only + // An input loses its value after becoming a radio + input = document.createElement( "input" ); + input.value = "t"; + input.type = "radio"; + support.radioValue = input.value === "t"; +} )(); + + +var boolHook, + attrHandle = jQuery.expr.attrHandle; + +jQuery.fn.extend( { + attr: function( name, value ) { + return access( this, jQuery.attr, name, value, arguments.length > 1 ); + }, + + removeAttr: function( name ) { + return this.each( function() { + jQuery.removeAttr( this, name ); + } ); + } +} ); + +jQuery.extend( { + attr: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set attributes on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + // Fallback to prop when attributes are not supported + if ( typeof elem.getAttribute === "undefined" ) { + return jQuery.prop( elem, name, value ); + } + + // Attribute hooks are determined by the lowercase version + // Grab necessary hook if one is defined + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + hooks = jQuery.attrHooks[ name.toLowerCase() ] || + ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined ); + } + + if ( value !== undefined ) { + if ( value === null ) { + jQuery.removeAttr( elem, name ); + return; + } + + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + elem.setAttribute( name, value + "" ); + return value; + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + ret = jQuery.find.attr( elem, name ); + + // Non-existent attributes return null, we normalize to undefined + return ret == null ? undefined : ret; + }, + + attrHooks: { + type: { + set: function( elem, value ) { + if ( !support.radioValue && value === "radio" && + nodeName( elem, "input" ) ) { + var val = elem.value; + elem.setAttribute( "type", value ); + if ( val ) { + elem.value = val; + } + return value; + } + } + } + }, + + removeAttr: function( elem, value ) { + var name, + i = 0, + + // Attribute names can contain non-HTML whitespace characters + // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2 + attrNames = value && value.match( rnothtmlwhite ); + + if ( attrNames && elem.nodeType === 1 ) { + while ( ( name = attrNames[ i++ ] ) ) { + elem.removeAttribute( name ); + } + } + } +} ); + +// Hooks for boolean attributes +boolHook = { + set: function( elem, value, name ) { + if ( value === false ) { + + // Remove boolean attributes when set to false + jQuery.removeAttr( elem, name ); + } else { + elem.setAttribute( name, name ); + } + return name; + } +}; + +jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( _i, name ) { + var getter = attrHandle[ name ] || jQuery.find.attr; + + attrHandle[ name ] = function( elem, name, isXML ) { + var ret, handle, + lowercaseName = name.toLowerCase(); + + if ( !isXML ) { + + // Avoid an infinite loop by temporarily removing this function from the getter + handle = attrHandle[ lowercaseName ]; + attrHandle[ lowercaseName ] = ret; + ret = getter( elem, name, isXML ) != null ? + lowercaseName : + null; + attrHandle[ lowercaseName ] = handle; + } + return ret; + }; +} ); + + + + +var rfocusable = /^(?:input|select|textarea|button)$/i, + rclickable = /^(?:a|area)$/i; + +jQuery.fn.extend( { + prop: function( name, value ) { + return access( this, jQuery.prop, name, value, arguments.length > 1 ); + }, + + removeProp: function( name ) { + return this.each( function() { + delete this[ jQuery.propFix[ name ] || name ]; + } ); + } +} ); + +jQuery.extend( { + prop: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set properties on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + + // Fix name and attach hooks + name = jQuery.propFix[ name ] || name; + hooks = jQuery.propHooks[ name ]; + } + + if ( value !== undefined ) { + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + return ( elem[ name ] = value ); + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + return elem[ name ]; + }, + + propHooks: { + tabIndex: { + get: function( elem ) { + + // Support: IE <=9 - 11 only + // elem.tabIndex doesn't always return the + // correct value when it hasn't been explicitly set + // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ + // Use proper attribute retrieval(#12072) + var tabindex = jQuery.find.attr( elem, "tabindex" ); + + if ( tabindex ) { + return parseInt( tabindex, 10 ); + } + + if ( + rfocusable.test( elem.nodeName ) || + rclickable.test( elem.nodeName ) && + elem.href + ) { + return 0; + } + + return -1; + } + } + }, + + propFix: { + "for": "htmlFor", + "class": "className" + } +} ); + +// Support: IE <=11 only +// Accessing the selectedIndex property +// forces the browser to respect setting selected +// on the option +// The getter ensures a default option is selected +// when in an optgroup +// eslint rule "no-unused-expressions" is disabled for this code +// since it considers such accessions noop +if ( !support.optSelected ) { + jQuery.propHooks.selected = { + get: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent && parent.parentNode ) { + parent.parentNode.selectedIndex; + } + return null; + }, + set: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent ) { + parent.selectedIndex; + + if ( parent.parentNode ) { + parent.parentNode.selectedIndex; + } + } + } + }; +} + +jQuery.each( [ + "tabIndex", + "readOnly", + "maxLength", + "cellSpacing", + "cellPadding", + "rowSpan", + "colSpan", + "useMap", + "frameBorder", + "contentEditable" +], function() { + jQuery.propFix[ this.toLowerCase() ] = this; +} ); + + + + + // Strip and collapse whitespace according to HTML spec + // https://infra.spec.whatwg.org/#strip-and-collapse-ascii-whitespace + function stripAndCollapse( value ) { + var tokens = value.match( rnothtmlwhite ) || []; + return tokens.join( " " ); + } + + +function getClass( elem ) { + return elem.getAttribute && elem.getAttribute( "class" ) || ""; +} + +function classesToArray( value ) { + if ( Array.isArray( value ) ) { + return value; + } + if ( typeof value === "string" ) { + return value.match( rnothtmlwhite ) || []; + } + return []; +} + +jQuery.fn.extend( { + addClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).addClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + classes = classesToArray( value ); + + if ( classes.length ) { + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + if ( cur.indexOf( " " + clazz + " " ) < 0 ) { + cur += clazz + " "; + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + removeClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + if ( !arguments.length ) { + return this.attr( "class", "" ); + } + + classes = classesToArray( value ); + + if ( classes.length ) { + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + + // This expression is here for better compressibility (see addClass) + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + + // Remove *all* instances + while ( cur.indexOf( " " + clazz + " " ) > -1 ) { + cur = cur.replace( " " + clazz + " ", " " ); + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + toggleClass: function( value, stateVal ) { + var type = typeof value, + isValidValue = type === "string" || Array.isArray( value ); + + if ( typeof stateVal === "boolean" && isValidValue ) { + return stateVal ? this.addClass( value ) : this.removeClass( value ); + } + + if ( isFunction( value ) ) { + return this.each( function( i ) { + jQuery( this ).toggleClass( + value.call( this, i, getClass( this ), stateVal ), + stateVal + ); + } ); + } + + return this.each( function() { + var className, i, self, classNames; + + if ( isValidValue ) { + + // Toggle individual class names + i = 0; + self = jQuery( this ); + classNames = classesToArray( value ); + + while ( ( className = classNames[ i++ ] ) ) { + + // Check each className given, space separated list + if ( self.hasClass( className ) ) { + self.removeClass( className ); + } else { + self.addClass( className ); + } + } + + // Toggle whole class name + } else if ( value === undefined || type === "boolean" ) { + className = getClass( this ); + if ( className ) { + + // Store className if set + dataPriv.set( this, "__className__", className ); + } + + // If the element has a class name or if we're passed `false`, + // then remove the whole classname (if there was one, the above saved it). + // Otherwise bring back whatever was previously saved (if anything), + // falling back to the empty string if nothing was stored. + if ( this.setAttribute ) { + this.setAttribute( "class", + className || value === false ? + "" : + dataPriv.get( this, "__className__" ) || "" + ); + } + } + } ); + }, + + hasClass: function( selector ) { + var className, elem, + i = 0; + + className = " " + selector + " "; + while ( ( elem = this[ i++ ] ) ) { + if ( elem.nodeType === 1 && + ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) { + return true; + } + } + + return false; + } +} ); + + + + +var rreturn = /\r/g; + +jQuery.fn.extend( { + val: function( value ) { + var hooks, ret, valueIsFunction, + elem = this[ 0 ]; + + if ( !arguments.length ) { + if ( elem ) { + hooks = jQuery.valHooks[ elem.type ] || + jQuery.valHooks[ elem.nodeName.toLowerCase() ]; + + if ( hooks && + "get" in hooks && + ( ret = hooks.get( elem, "value" ) ) !== undefined + ) { + return ret; + } + + ret = elem.value; + + // Handle most common string cases + if ( typeof ret === "string" ) { + return ret.replace( rreturn, "" ); + } + + // Handle cases where value is null/undef or number + return ret == null ? "" : ret; + } + + return; + } + + valueIsFunction = isFunction( value ); + + return this.each( function( i ) { + var val; + + if ( this.nodeType !== 1 ) { + return; + } + + if ( valueIsFunction ) { + val = value.call( this, i, jQuery( this ).val() ); + } else { + val = value; + } + + // Treat null/undefined as ""; convert numbers to string + if ( val == null ) { + val = ""; + + } else if ( typeof val === "number" ) { + val += ""; + + } else if ( Array.isArray( val ) ) { + val = jQuery.map( val, function( value ) { + return value == null ? "" : value + ""; + } ); + } + + hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; + + // If set returns undefined, fall back to normal setting + if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) { + this.value = val; + } + } ); + } +} ); + +jQuery.extend( { + valHooks: { + option: { + get: function( elem ) { + + var val = jQuery.find.attr( elem, "value" ); + return val != null ? + val : + + // Support: IE <=10 - 11 only + // option.text throws exceptions (#14686, #14858) + // Strip and collapse whitespace + // https://html.spec.whatwg.org/#strip-and-collapse-whitespace + stripAndCollapse( jQuery.text( elem ) ); + } + }, + select: { + get: function( elem ) { + var value, option, i, + options = elem.options, + index = elem.selectedIndex, + one = elem.type === "select-one", + values = one ? null : [], + max = one ? index + 1 : options.length; + + if ( index < 0 ) { + i = max; + + } else { + i = one ? index : 0; + } + + // Loop through all the selected options + for ( ; i < max; i++ ) { + option = options[ i ]; + + // Support: IE <=9 only + // IE8-9 doesn't update selected after form reset (#2551) + if ( ( option.selected || i === index ) && + + // Don't return options that are disabled or in a disabled optgroup + !option.disabled && + ( !option.parentNode.disabled || + !nodeName( option.parentNode, "optgroup" ) ) ) { + + // Get the specific value for the option + value = jQuery( option ).val(); + + // We don't need an array for one selects + if ( one ) { + return value; + } + + // Multi-Selects return an array + values.push( value ); + } + } + + return values; + }, + + set: function( elem, value ) { + var optionSet, option, + options = elem.options, + values = jQuery.makeArray( value ), + i = options.length; + + while ( i-- ) { + option = options[ i ]; + + /* eslint-disable no-cond-assign */ + + if ( option.selected = + jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1 + ) { + optionSet = true; + } + + /* eslint-enable no-cond-assign */ + } + + // Force browsers to behave consistently when non-matching value is set + if ( !optionSet ) { + elem.selectedIndex = -1; + } + return values; + } + } + } +} ); + +// Radios and checkboxes getter/setter +jQuery.each( [ "radio", "checkbox" ], function() { + jQuery.valHooks[ this ] = { + set: function( elem, value ) { + if ( Array.isArray( value ) ) { + return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 ); + } + } + }; + if ( !support.checkOn ) { + jQuery.valHooks[ this ].get = function( elem ) { + return elem.getAttribute( "value" ) === null ? "on" : elem.value; + }; + } +} ); + + + + +// Return jQuery for attributes-only inclusion + + +support.focusin = "onfocusin" in window; + + +var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, + stopPropagationCallback = function( e ) { + e.stopPropagation(); + }; + +jQuery.extend( jQuery.event, { + + trigger: function( event, data, elem, onlyHandlers ) { + + var i, cur, tmp, bubbleType, ontype, handle, special, lastElement, + eventPath = [ elem || document ], + type = hasOwn.call( event, "type" ) ? event.type : event, + namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : []; + + cur = lastElement = tmp = elem = elem || document; + + // Don't do events on text and comment nodes + if ( elem.nodeType === 3 || elem.nodeType === 8 ) { + return; + } + + // focus/blur morphs to focusin/out; ensure we're not firing them right now + if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { + return; + } + + if ( type.indexOf( "." ) > -1 ) { + + // Namespaced trigger; create a regexp to match event type in handle() + namespaces = type.split( "." ); + type = namespaces.shift(); + namespaces.sort(); + } + ontype = type.indexOf( ":" ) < 0 && "on" + type; + + // Caller can pass in a jQuery.Event object, Object, or just an event type string + event = event[ jQuery.expando ] ? + event : + new jQuery.Event( type, typeof event === "object" && event ); + + // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) + event.isTrigger = onlyHandlers ? 2 : 3; + event.namespace = namespaces.join( "." ); + event.rnamespace = event.namespace ? + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) : + null; + + // Clean up the event in case it is being reused + event.result = undefined; + if ( !event.target ) { + event.target = elem; + } + + // Clone any incoming data and prepend the event, creating the handler arg list + data = data == null ? + [ event ] : + jQuery.makeArray( data, [ event ] ); + + // Allow special events to draw outside the lines + special = jQuery.event.special[ type ] || {}; + if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) { + return; + } + + // Determine event propagation path in advance, per W3C events spec (#9951) + // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) + if ( !onlyHandlers && !special.noBubble && !isWindow( elem ) ) { + + bubbleType = special.delegateType || type; + if ( !rfocusMorph.test( bubbleType + type ) ) { + cur = cur.parentNode; + } + for ( ; cur; cur = cur.parentNode ) { + eventPath.push( cur ); + tmp = cur; + } + + // Only add window if we got to document (e.g., not plain obj or detached DOM) + if ( tmp === ( elem.ownerDocument || document ) ) { + eventPath.push( tmp.defaultView || tmp.parentWindow || window ); + } + } + + // Fire handlers on the event path + i = 0; + while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) { + lastElement = cur; + event.type = i > 1 ? + bubbleType : + special.bindType || type; + + // jQuery handler + handle = ( + dataPriv.get( cur, "events" ) || Object.create( null ) + )[ event.type ] && + dataPriv.get( cur, "handle" ); + if ( handle ) { + handle.apply( cur, data ); + } + + // Native handler + handle = ontype && cur[ ontype ]; + if ( handle && handle.apply && acceptData( cur ) ) { + event.result = handle.apply( cur, data ); + if ( event.result === false ) { + event.preventDefault(); + } + } + } + event.type = type; + + // If nobody prevented the default action, do it now + if ( !onlyHandlers && !event.isDefaultPrevented() ) { + + if ( ( !special._default || + special._default.apply( eventPath.pop(), data ) === false ) && + acceptData( elem ) ) { + + // Call a native DOM method on the target with the same name as the event. + // Don't do default actions on window, that's where global variables be (#6170) + if ( ontype && isFunction( elem[ type ] ) && !isWindow( elem ) ) { + + // Don't re-trigger an onFOO event when we call its FOO() method + tmp = elem[ ontype ]; + + if ( tmp ) { + elem[ ontype ] = null; + } + + // Prevent re-triggering of the same event, since we already bubbled it above + jQuery.event.triggered = type; + + if ( event.isPropagationStopped() ) { + lastElement.addEventListener( type, stopPropagationCallback ); + } + + elem[ type ](); + + if ( event.isPropagationStopped() ) { + lastElement.removeEventListener( type, stopPropagationCallback ); + } + + jQuery.event.triggered = undefined; + + if ( tmp ) { + elem[ ontype ] = tmp; + } + } + } + } + + return event.result; + }, + + // Piggyback on a donor event to simulate a different one + // Used only for `focus(in | out)` events + simulate: function( type, elem, event ) { + var e = jQuery.extend( + new jQuery.Event(), + event, + { + type: type, + isSimulated: true + } + ); + + jQuery.event.trigger( e, null, elem ); + } + +} ); + +jQuery.fn.extend( { + + trigger: function( type, data ) { + return this.each( function() { + jQuery.event.trigger( type, data, this ); + } ); + }, + triggerHandler: function( type, data ) { + var elem = this[ 0 ]; + if ( elem ) { + return jQuery.event.trigger( type, data, elem, true ); + } + } +} ); + + +// Support: Firefox <=44 +// Firefox doesn't have focus(in | out) events +// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787 +// +// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1 +// focus(in | out) events fire after focus & blur events, +// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order +// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857 +if ( !support.focusin ) { + jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) { + + // Attach a single capturing handler on the document while someone wants focusin/focusout + var handler = function( event ) { + jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) ); + }; + + jQuery.event.special[ fix ] = { + setup: function() { + + // Handle: regular nodes (via `this.ownerDocument`), window + // (via `this.document`) & document (via `this`). + var doc = this.ownerDocument || this.document || this, + attaches = dataPriv.access( doc, fix ); + + if ( !attaches ) { + doc.addEventListener( orig, handler, true ); + } + dataPriv.access( doc, fix, ( attaches || 0 ) + 1 ); + }, + teardown: function() { + var doc = this.ownerDocument || this.document || this, + attaches = dataPriv.access( doc, fix ) - 1; + + if ( !attaches ) { + doc.removeEventListener( orig, handler, true ); + dataPriv.remove( doc, fix ); + + } else { + dataPriv.access( doc, fix, attaches ); + } + } + }; + } ); +} +var location = window.location; + +var nonce = { guid: Date.now() }; + +var rquery = ( /\?/ ); + + + +// Cross-browser xml parsing +jQuery.parseXML = function( data ) { + var xml; + if ( !data || typeof data !== "string" ) { + return null; + } + + // Support: IE 9 - 11 only + // IE throws on parseFromString with invalid input. + try { + xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" ); + } catch ( e ) { + xml = undefined; + } + + if ( !xml || xml.getElementsByTagName( "parsererror" ).length ) { + jQuery.error( "Invalid XML: " + data ); + } + return xml; +}; + + +var + rbracket = /\[\]$/, + rCRLF = /\r?\n/g, + rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i, + rsubmittable = /^(?:input|select|textarea|keygen)/i; + +function buildParams( prefix, obj, traditional, add ) { + var name; + + if ( Array.isArray( obj ) ) { + + // Serialize array item. + jQuery.each( obj, function( i, v ) { + if ( traditional || rbracket.test( prefix ) ) { + + // Treat each array item as a scalar. + add( prefix, v ); + + } else { + + // Item is non-scalar (array or object), encode its numeric index. + buildParams( + prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]", + v, + traditional, + add + ); + } + } ); + + } else if ( !traditional && toType( obj ) === "object" ) { + + // Serialize object item. + for ( name in obj ) { + buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); + } + + } else { + + // Serialize scalar item. + add( prefix, obj ); + } +} + +// Serialize an array of form elements or a set of +// key/values into a query string +jQuery.param = function( a, traditional ) { + var prefix, + s = [], + add = function( key, valueOrFunction ) { + + // If value is a function, invoke it and use its return value + var value = isFunction( valueOrFunction ) ? + valueOrFunction() : + valueOrFunction; + + s[ s.length ] = encodeURIComponent( key ) + "=" + + encodeURIComponent( value == null ? "" : value ); + }; + + if ( a == null ) { + return ""; + } + + // If an array was passed in, assume that it is an array of form elements. + if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { + + // Serialize the form elements + jQuery.each( a, function() { + add( this.name, this.value ); + } ); + + } else { + + // If traditional, encode the "old" way (the way 1.3.2 or older + // did it), otherwise encode params recursively. + for ( prefix in a ) { + buildParams( prefix, a[ prefix ], traditional, add ); + } + } + + // Return the resulting serialization + return s.join( "&" ); +}; + +jQuery.fn.extend( { + serialize: function() { + return jQuery.param( this.serializeArray() ); + }, + serializeArray: function() { + return this.map( function() { + + // Can add propHook for "elements" to filter or add form elements + var elements = jQuery.prop( this, "elements" ); + return elements ? jQuery.makeArray( elements ) : this; + } ) + .filter( function() { + var type = this.type; + + // Use .is( ":disabled" ) so that fieldset[disabled] works + return this.name && !jQuery( this ).is( ":disabled" ) && + rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) && + ( this.checked || !rcheckableType.test( type ) ); + } ) + .map( function( _i, elem ) { + var val = jQuery( this ).val(); + + if ( val == null ) { + return null; + } + + if ( Array.isArray( val ) ) { + return jQuery.map( val, function( val ) { + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ); + } + + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ).get(); + } +} ); + + +var + r20 = /%20/g, + rhash = /#.*$/, + rantiCache = /([?&])_=[^&]*/, + rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg, + + // #7653, #8125, #8152: local protocol detection + rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/, + rnoContent = /^(?:GET|HEAD)$/, + rprotocol = /^\/\//, + + /* Prefilters + * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example) + * 2) These are called: + * - BEFORE asking for a transport + * - AFTER param serialization (s.data is a string if s.processData is true) + * 3) key is the dataType + * 4) the catchall symbol "*" can be used + * 5) execution will start with transport dataType and THEN continue down to "*" if needed + */ + prefilters = {}, + + /* Transports bindings + * 1) key is the dataType + * 2) the catchall symbol "*" can be used + * 3) selection will start with transport dataType and THEN go to "*" if needed + */ + transports = {}, + + // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression + allTypes = "*/".concat( "*" ), + + // Anchor tag for parsing the document origin + originAnchor = document.createElement( "a" ); + originAnchor.href = location.href; + +// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport +function addToPrefiltersOrTransports( structure ) { + + // dataTypeExpression is optional and defaults to "*" + return function( dataTypeExpression, func ) { + + if ( typeof dataTypeExpression !== "string" ) { + func = dataTypeExpression; + dataTypeExpression = "*"; + } + + var dataType, + i = 0, + dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || []; + + if ( isFunction( func ) ) { + + // For each dataType in the dataTypeExpression + while ( ( dataType = dataTypes[ i++ ] ) ) { + + // Prepend if requested + if ( dataType[ 0 ] === "+" ) { + dataType = dataType.slice( 1 ) || "*"; + ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func ); + + // Otherwise append + } else { + ( structure[ dataType ] = structure[ dataType ] || [] ).push( func ); + } + } + } + }; +} + +// Base inspection function for prefilters and transports +function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) { + + var inspected = {}, + seekingTransport = ( structure === transports ); + + function inspect( dataType ) { + var selected; + inspected[ dataType ] = true; + jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) { + var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR ); + if ( typeof dataTypeOrTransport === "string" && + !seekingTransport && !inspected[ dataTypeOrTransport ] ) { + + options.dataTypes.unshift( dataTypeOrTransport ); + inspect( dataTypeOrTransport ); + return false; + } else if ( seekingTransport ) { + return !( selected = dataTypeOrTransport ); + } + } ); + return selected; + } + + return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" ); +} + +// A special extend for ajax options +// that takes "flat" options (not to be deep extended) +// Fixes #9887 +function ajaxExtend( target, src ) { + var key, deep, + flatOptions = jQuery.ajaxSettings.flatOptions || {}; + + for ( key in src ) { + if ( src[ key ] !== undefined ) { + ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ]; + } + } + if ( deep ) { + jQuery.extend( true, target, deep ); + } + + return target; +} + +/* Handles responses to an ajax request: + * - finds the right dataType (mediates between content-type and expected dataType) + * - returns the corresponding response + */ +function ajaxHandleResponses( s, jqXHR, responses ) { + + var ct, type, finalDataType, firstDataType, + contents = s.contents, + dataTypes = s.dataTypes; + + // Remove auto dataType and get content-type in the process + while ( dataTypes[ 0 ] === "*" ) { + dataTypes.shift(); + if ( ct === undefined ) { + ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" ); + } + } + + // Check if we're dealing with a known content-type + if ( ct ) { + for ( type in contents ) { + if ( contents[ type ] && contents[ type ].test( ct ) ) { + dataTypes.unshift( type ); + break; + } + } + } + + // Check to see if we have a response for the expected dataType + if ( dataTypes[ 0 ] in responses ) { + finalDataType = dataTypes[ 0 ]; + } else { + + // Try convertible dataTypes + for ( type in responses ) { + if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) { + finalDataType = type; + break; + } + if ( !firstDataType ) { + firstDataType = type; + } + } + + // Or just use first one + finalDataType = finalDataType || firstDataType; + } + + // If we found a dataType + // We add the dataType to the list if needed + // and return the corresponding response + if ( finalDataType ) { + if ( finalDataType !== dataTypes[ 0 ] ) { + dataTypes.unshift( finalDataType ); + } + return responses[ finalDataType ]; + } +} + +/* Chain conversions given the request and the original response + * Also sets the responseXXX fields on the jqXHR instance + */ +function ajaxConvert( s, response, jqXHR, isSuccess ) { + var conv2, current, conv, tmp, prev, + converters = {}, + + // Work with a copy of dataTypes in case we need to modify it for conversion + dataTypes = s.dataTypes.slice(); + + // Create converters map with lowercased keys + if ( dataTypes[ 1 ] ) { + for ( conv in s.converters ) { + converters[ conv.toLowerCase() ] = s.converters[ conv ]; + } + } + + current = dataTypes.shift(); + + // Convert to each sequential dataType + while ( current ) { + + if ( s.responseFields[ current ] ) { + jqXHR[ s.responseFields[ current ] ] = response; + } + + // Apply the dataFilter if provided + if ( !prev && isSuccess && s.dataFilter ) { + response = s.dataFilter( response, s.dataType ); + } + + prev = current; + current = dataTypes.shift(); + + if ( current ) { + + // There's only work to do if current dataType is non-auto + if ( current === "*" ) { + + current = prev; + + // Convert response if prev dataType is non-auto and differs from current + } else if ( prev !== "*" && prev !== current ) { + + // Seek a direct converter + conv = converters[ prev + " " + current ] || converters[ "* " + current ]; + + // If none found, seek a pair + if ( !conv ) { + for ( conv2 in converters ) { + + // If conv2 outputs current + tmp = conv2.split( " " ); + if ( tmp[ 1 ] === current ) { + + // If prev can be converted to accepted input + conv = converters[ prev + " " + tmp[ 0 ] ] || + converters[ "* " + tmp[ 0 ] ]; + if ( conv ) { + + // Condense equivalence converters + if ( conv === true ) { + conv = converters[ conv2 ]; + + // Otherwise, insert the intermediate dataType + } else if ( converters[ conv2 ] !== true ) { + current = tmp[ 0 ]; + dataTypes.unshift( tmp[ 1 ] ); + } + break; + } + } + } + } + + // Apply converter (if not an equivalence) + if ( conv !== true ) { + + // Unless errors are allowed to bubble, catch and return them + if ( conv && s.throws ) { + response = conv( response ); + } else { + try { + response = conv( response ); + } catch ( e ) { + return { + state: "parsererror", + error: conv ? e : "No conversion from " + prev + " to " + current + }; + } + } + } + } + } + } + + return { state: "success", data: response }; +} + +jQuery.extend( { + + // Counter for holding the number of active queries + active: 0, + + // Last-Modified header cache for next request + lastModified: {}, + etag: {}, + + ajaxSettings: { + url: location.href, + type: "GET", + isLocal: rlocalProtocol.test( location.protocol ), + global: true, + processData: true, + async: true, + contentType: "application/x-www-form-urlencoded; charset=UTF-8", + + /* + timeout: 0, + data: null, + dataType: null, + username: null, + password: null, + cache: null, + throws: false, + traditional: false, + headers: {}, + */ + + accepts: { + "*": allTypes, + text: "text/plain", + html: "text/html", + xml: "application/xml, text/xml", + json: "application/json, text/javascript" + }, + + contents: { + xml: /\bxml\b/, + html: /\bhtml/, + json: /\bjson\b/ + }, + + responseFields: { + xml: "responseXML", + text: "responseText", + json: "responseJSON" + }, + + // Data converters + // Keys separate source (or catchall "*") and destination types with a single space + converters: { + + // Convert anything to text + "* text": String, + + // Text to html (true = no transformation) + "text html": true, + + // Evaluate text as a json expression + "text json": JSON.parse, + + // Parse text as xml + "text xml": jQuery.parseXML + }, + + // For options that shouldn't be deep extended: + // you can add your own custom options here if + // and when you create one that shouldn't be + // deep extended (see ajaxExtend) + flatOptions: { + url: true, + context: true + } + }, + + // Creates a full fledged settings object into target + // with both ajaxSettings and settings fields. + // If target is omitted, writes into ajaxSettings. + ajaxSetup: function( target, settings ) { + return settings ? + + // Building a settings object + ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) : + + // Extending ajaxSettings + ajaxExtend( jQuery.ajaxSettings, target ); + }, + + ajaxPrefilter: addToPrefiltersOrTransports( prefilters ), + ajaxTransport: addToPrefiltersOrTransports( transports ), + + // Main method + ajax: function( url, options ) { + + // If url is an object, simulate pre-1.5 signature + if ( typeof url === "object" ) { + options = url; + url = undefined; + } + + // Force options to be an object + options = options || {}; + + var transport, + + // URL without anti-cache param + cacheURL, + + // Response headers + responseHeadersString, + responseHeaders, + + // timeout handle + timeoutTimer, + + // Url cleanup var + urlAnchor, + + // Request state (becomes false upon send and true upon completion) + completed, + + // To know if global events are to be dispatched + fireGlobals, + + // Loop variable + i, + + // uncached part of the url + uncached, + + // Create the final options object + s = jQuery.ajaxSetup( {}, options ), + + // Callbacks context + callbackContext = s.context || s, + + // Context for global events is callbackContext if it is a DOM node or jQuery collection + globalEventContext = s.context && + ( callbackContext.nodeType || callbackContext.jquery ) ? + jQuery( callbackContext ) : + jQuery.event, + + // Deferreds + deferred = jQuery.Deferred(), + completeDeferred = jQuery.Callbacks( "once memory" ), + + // Status-dependent callbacks + statusCode = s.statusCode || {}, + + // Headers (they are sent all at once) + requestHeaders = {}, + requestHeadersNames = {}, + + // Default abort message + strAbort = "canceled", + + // Fake xhr + jqXHR = { + readyState: 0, + + // Builds headers hashtable if needed + getResponseHeader: function( key ) { + var match; + if ( completed ) { + if ( !responseHeaders ) { + responseHeaders = {}; + while ( ( match = rheaders.exec( responseHeadersString ) ) ) { + responseHeaders[ match[ 1 ].toLowerCase() + " " ] = + ( responseHeaders[ match[ 1 ].toLowerCase() + " " ] || [] ) + .concat( match[ 2 ] ); + } + } + match = responseHeaders[ key.toLowerCase() + " " ]; + } + return match == null ? null : match.join( ", " ); + }, + + // Raw string + getAllResponseHeaders: function() { + return completed ? responseHeadersString : null; + }, + + // Caches the header + setRequestHeader: function( name, value ) { + if ( completed == null ) { + name = requestHeadersNames[ name.toLowerCase() ] = + requestHeadersNames[ name.toLowerCase() ] || name; + requestHeaders[ name ] = value; + } + return this; + }, + + // Overrides response content-type header + overrideMimeType: function( type ) { + if ( completed == null ) { + s.mimeType = type; + } + return this; + }, + + // Status-dependent callbacks + statusCode: function( map ) { + var code; + if ( map ) { + if ( completed ) { + + // Execute the appropriate callbacks + jqXHR.always( map[ jqXHR.status ] ); + } else { + + // Lazy-add the new callbacks in a way that preserves old ones + for ( code in map ) { + statusCode[ code ] = [ statusCode[ code ], map[ code ] ]; + } + } + } + return this; + }, + + // Cancel the request + abort: function( statusText ) { + var finalText = statusText || strAbort; + if ( transport ) { + transport.abort( finalText ); + } + done( 0, finalText ); + return this; + } + }; + + // Attach deferreds + deferred.promise( jqXHR ); + + // Add protocol if not provided (prefilters might expect it) + // Handle falsy url in the settings object (#10093: consistency with old signature) + // We also use the url parameter if available + s.url = ( ( url || s.url || location.href ) + "" ) + .replace( rprotocol, location.protocol + "//" ); + + // Alias method option to type as per ticket #12004 + s.type = options.method || options.type || s.method || s.type; + + // Extract dataTypes list + s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ]; + + // A cross-domain request is in order when the origin doesn't match the current origin. + if ( s.crossDomain == null ) { + urlAnchor = document.createElement( "a" ); + + // Support: IE <=8 - 11, Edge 12 - 15 + // IE throws exception on accessing the href property if url is malformed, + // e.g. http://example.com:80x/ + try { + urlAnchor.href = s.url; + + // Support: IE <=8 - 11 only + // Anchor's host property isn't correctly set when s.url is relative + urlAnchor.href = urlAnchor.href; + s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !== + urlAnchor.protocol + "//" + urlAnchor.host; + } catch ( e ) { + + // If there is an error parsing the URL, assume it is crossDomain, + // it can be rejected by the transport if it is invalid + s.crossDomain = true; + } + } + + // Convert data if not already a string + if ( s.data && s.processData && typeof s.data !== "string" ) { + s.data = jQuery.param( s.data, s.traditional ); + } + + // Apply prefilters + inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); + + // If request was aborted inside a prefilter, stop there + if ( completed ) { + return jqXHR; + } + + // We can fire global events as of now if asked to + // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118) + fireGlobals = jQuery.event && s.global; + + // Watch for a new set of requests + if ( fireGlobals && jQuery.active++ === 0 ) { + jQuery.event.trigger( "ajaxStart" ); + } + + // Uppercase the type + s.type = s.type.toUpperCase(); + + // Determine if request has content + s.hasContent = !rnoContent.test( s.type ); + + // Save the URL in case we're toying with the If-Modified-Since + // and/or If-None-Match header later on + // Remove hash to simplify url manipulation + cacheURL = s.url.replace( rhash, "" ); + + // More options handling for requests with no content + if ( !s.hasContent ) { + + // Remember the hash so we can put it back + uncached = s.url.slice( cacheURL.length ); + + // If data is available and should be processed, append data to url + if ( s.data && ( s.processData || typeof s.data === "string" ) ) { + cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data; + + // #9682: remove data so that it's not used in an eventual retry + delete s.data; + } + + // Add or update anti-cache param if needed + if ( s.cache === false ) { + cacheURL = cacheURL.replace( rantiCache, "$1" ); + uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce.guid++ ) + + uncached; + } + + // Put hash and anti-cache on the URL that will be requested (gh-1732) + s.url = cacheURL + uncached; + + // Change '%20' to '+' if this is encoded form body content (gh-2658) + } else if ( s.data && s.processData && + ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) { + s.data = s.data.replace( r20, "+" ); + } + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + if ( jQuery.lastModified[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] ); + } + if ( jQuery.etag[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] ); + } + } + + // Set the correct header, if data is being sent + if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { + jqXHR.setRequestHeader( "Content-Type", s.contentType ); + } + + // Set the Accepts header for the server, depending on the dataType + jqXHR.setRequestHeader( + "Accept", + s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ? + s.accepts[ s.dataTypes[ 0 ] ] + + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) : + s.accepts[ "*" ] + ); + + // Check for headers option + for ( i in s.headers ) { + jqXHR.setRequestHeader( i, s.headers[ i ] ); + } + + // Allow custom headers/mimetypes and early abort + if ( s.beforeSend && + ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) { + + // Abort if not done already and return + return jqXHR.abort(); + } + + // Aborting is no longer a cancellation + strAbort = "abort"; + + // Install callbacks on deferreds + completeDeferred.add( s.complete ); + jqXHR.done( s.success ); + jqXHR.fail( s.error ); + + // Get transport + transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); + + // If no transport, we auto-abort + if ( !transport ) { + done( -1, "No Transport" ); + } else { + jqXHR.readyState = 1; + + // Send global event + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); + } + + // If request was aborted inside ajaxSend, stop there + if ( completed ) { + return jqXHR; + } + + // Timeout + if ( s.async && s.timeout > 0 ) { + timeoutTimer = window.setTimeout( function() { + jqXHR.abort( "timeout" ); + }, s.timeout ); + } + + try { + completed = false; + transport.send( requestHeaders, done ); + } catch ( e ) { + + // Rethrow post-completion exceptions + if ( completed ) { + throw e; + } + + // Propagate others as results + done( -1, e ); + } + } + + // Callback for when everything is done + function done( status, nativeStatusText, responses, headers ) { + var isSuccess, success, error, response, modified, + statusText = nativeStatusText; + + // Ignore repeat invocations + if ( completed ) { + return; + } + + completed = true; + + // Clear timeout if it exists + if ( timeoutTimer ) { + window.clearTimeout( timeoutTimer ); + } + + // Dereference transport for early garbage collection + // (no matter how long the jqXHR object will be used) + transport = undefined; + + // Cache response headers + responseHeadersString = headers || ""; + + // Set readyState + jqXHR.readyState = status > 0 ? 4 : 0; + + // Determine if successful + isSuccess = status >= 200 && status < 300 || status === 304; + + // Get response data + if ( responses ) { + response = ajaxHandleResponses( s, jqXHR, responses ); + } + + // Use a noop converter for missing script + if ( !isSuccess && jQuery.inArray( "script", s.dataTypes ) > -1 ) { + s.converters[ "text script" ] = function() {}; + } + + // Convert no matter what (that way responseXXX fields are always set) + response = ajaxConvert( s, response, jqXHR, isSuccess ); + + // If successful, handle type chaining + if ( isSuccess ) { + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + modified = jqXHR.getResponseHeader( "Last-Modified" ); + if ( modified ) { + jQuery.lastModified[ cacheURL ] = modified; + } + modified = jqXHR.getResponseHeader( "etag" ); + if ( modified ) { + jQuery.etag[ cacheURL ] = modified; + } + } + + // if no content + if ( status === 204 || s.type === "HEAD" ) { + statusText = "nocontent"; + + // if not modified + } else if ( status === 304 ) { + statusText = "notmodified"; + + // If we have data, let's convert it + } else { + statusText = response.state; + success = response.data; + error = response.error; + isSuccess = !error; + } + } else { + + // Extract error from statusText and normalize for non-aborts + error = statusText; + if ( status || !statusText ) { + statusText = "error"; + if ( status < 0 ) { + status = 0; + } + } + } + + // Set data for the fake xhr object + jqXHR.status = status; + jqXHR.statusText = ( nativeStatusText || statusText ) + ""; + + // Success/Error + if ( isSuccess ) { + deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); + } else { + deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); + } + + // Status-dependent callbacks + jqXHR.statusCode( statusCode ); + statusCode = undefined; + + if ( fireGlobals ) { + globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError", + [ jqXHR, s, isSuccess ? success : error ] ); + } + + // Complete + completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] ); + + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] ); + + // Handle the global AJAX counter + if ( !( --jQuery.active ) ) { + jQuery.event.trigger( "ajaxStop" ); + } + } + } + + return jqXHR; + }, + + getJSON: function( url, data, callback ) { + return jQuery.get( url, data, callback, "json" ); + }, + + getScript: function( url, callback ) { + return jQuery.get( url, undefined, callback, "script" ); + } +} ); + +jQuery.each( [ "get", "post" ], function( _i, method ) { + jQuery[ method ] = function( url, data, callback, type ) { + + // Shift arguments if data argument was omitted + if ( isFunction( data ) ) { + type = type || callback; + callback = data; + data = undefined; + } + + // The url can be an options object (which then must have .url) + return jQuery.ajax( jQuery.extend( { + url: url, + type: method, + dataType: type, + data: data, + success: callback + }, jQuery.isPlainObject( url ) && url ) ); + }; +} ); + +jQuery.ajaxPrefilter( function( s ) { + var i; + for ( i in s.headers ) { + if ( i.toLowerCase() === "content-type" ) { + s.contentType = s.headers[ i ] || ""; + } + } +} ); + + +jQuery._evalUrl = function( url, options, doc ) { + return jQuery.ajax( { + url: url, + + // Make this explicit, since user can override this through ajaxSetup (#11264) + type: "GET", + dataType: "script", + cache: true, + async: false, + global: false, + + // Only evaluate the response if it is successful (gh-4126) + // dataFilter is not invoked for failure responses, so using it instead + // of the default converter is kludgy but it works. + converters: { + "text script": function() {} + }, + dataFilter: function( response ) { + jQuery.globalEval( response, options, doc ); + } + } ); +}; + + +jQuery.fn.extend( { + wrapAll: function( html ) { + var wrap; + + if ( this[ 0 ] ) { + if ( isFunction( html ) ) { + html = html.call( this[ 0 ] ); + } + + // The elements to wrap the target around + wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true ); + + if ( this[ 0 ].parentNode ) { + wrap.insertBefore( this[ 0 ] ); + } + + wrap.map( function() { + var elem = this; + + while ( elem.firstElementChild ) { + elem = elem.firstElementChild; + } + + return elem; + } ).append( this ); + } + + return this; + }, + + wrapInner: function( html ) { + if ( isFunction( html ) ) { + return this.each( function( i ) { + jQuery( this ).wrapInner( html.call( this, i ) ); + } ); + } + + return this.each( function() { + var self = jQuery( this ), + contents = self.contents(); + + if ( contents.length ) { + contents.wrapAll( html ); + + } else { + self.append( html ); + } + } ); + }, + + wrap: function( html ) { + var htmlIsFunction = isFunction( html ); + + return this.each( function( i ) { + jQuery( this ).wrapAll( htmlIsFunction ? html.call( this, i ) : html ); + } ); + }, + + unwrap: function( selector ) { + this.parent( selector ).not( "body" ).each( function() { + jQuery( this ).replaceWith( this.childNodes ); + } ); + return this; + } +} ); + + +jQuery.expr.pseudos.hidden = function( elem ) { + return !jQuery.expr.pseudos.visible( elem ); +}; +jQuery.expr.pseudos.visible = function( elem ) { + return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length ); +}; + + + + +jQuery.ajaxSettings.xhr = function() { + try { + return new window.XMLHttpRequest(); + } catch ( e ) {} +}; + +var xhrSuccessStatus = { + + // File protocol always yields status code 0, assume 200 + 0: 200, + + // Support: IE <=9 only + // #1450: sometimes IE returns 1223 when it should be 204 + 1223: 204 + }, + xhrSupported = jQuery.ajaxSettings.xhr(); + +support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported ); +support.ajax = xhrSupported = !!xhrSupported; + +jQuery.ajaxTransport( function( options ) { + var callback, errorCallback; + + // Cross domain only allowed if supported through XMLHttpRequest + if ( support.cors || xhrSupported && !options.crossDomain ) { + return { + send: function( headers, complete ) { + var i, + xhr = options.xhr(); + + xhr.open( + options.type, + options.url, + options.async, + options.username, + options.password + ); + + // Apply custom fields if provided + if ( options.xhrFields ) { + for ( i in options.xhrFields ) { + xhr[ i ] = options.xhrFields[ i ]; + } + } + + // Override mime type if needed + if ( options.mimeType && xhr.overrideMimeType ) { + xhr.overrideMimeType( options.mimeType ); + } + + // X-Requested-With header + // For cross-domain requests, seeing as conditions for a preflight are + // akin to a jigsaw puzzle, we simply never set it to be sure. + // (it can always be set on a per-request basis or even using ajaxSetup) + // For same-domain requests, won't change header if already provided. + if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) { + headers[ "X-Requested-With" ] = "XMLHttpRequest"; + } + + // Set headers + for ( i in headers ) { + xhr.setRequestHeader( i, headers[ i ] ); + } + + // Callback + callback = function( type ) { + return function() { + if ( callback ) { + callback = errorCallback = xhr.onload = + xhr.onerror = xhr.onabort = xhr.ontimeout = + xhr.onreadystatechange = null; + + if ( type === "abort" ) { + xhr.abort(); + } else if ( type === "error" ) { + + // Support: IE <=9 only + // On a manual native abort, IE9 throws + // errors on any property access that is not readyState + if ( typeof xhr.status !== "number" ) { + complete( 0, "error" ); + } else { + complete( + + // File: protocol always yields status 0; see #8605, #14207 + xhr.status, + xhr.statusText + ); + } + } else { + complete( + xhrSuccessStatus[ xhr.status ] || xhr.status, + xhr.statusText, + + // Support: IE <=9 only + // IE9 has no XHR2 but throws on binary (trac-11426) + // For XHR2 non-text, let the caller handle it (gh-2498) + ( xhr.responseType || "text" ) !== "text" || + typeof xhr.responseText !== "string" ? + { binary: xhr.response } : + { text: xhr.responseText }, + xhr.getAllResponseHeaders() + ); + } + } + }; + }; + + // Listen to events + xhr.onload = callback(); + errorCallback = xhr.onerror = xhr.ontimeout = callback( "error" ); + + // Support: IE 9 only + // Use onreadystatechange to replace onabort + // to handle uncaught aborts + if ( xhr.onabort !== undefined ) { + xhr.onabort = errorCallback; + } else { + xhr.onreadystatechange = function() { + + // Check readyState before timeout as it changes + if ( xhr.readyState === 4 ) { + + // Allow onerror to be called first, + // but that will not handle a native abort + // Also, save errorCallback to a variable + // as xhr.onerror cannot be accessed + window.setTimeout( function() { + if ( callback ) { + errorCallback(); + } + } ); + } + }; + } + + // Create the abort callback + callback = callback( "abort" ); + + try { + + // Do send the request (this may raise an exception) + xhr.send( options.hasContent && options.data || null ); + } catch ( e ) { + + // #14683: Only rethrow if this hasn't been notified as an error yet + if ( callback ) { + throw e; + } + } + }, + + abort: function() { + if ( callback ) { + callback(); + } + } + }; + } +} ); + + + + +// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432) +jQuery.ajaxPrefilter( function( s ) { + if ( s.crossDomain ) { + s.contents.script = false; + } +} ); + +// Install script dataType +jQuery.ajaxSetup( { + accepts: { + script: "text/javascript, application/javascript, " + + "application/ecmascript, application/x-ecmascript" + }, + contents: { + script: /\b(?:java|ecma)script\b/ + }, + converters: { + "text script": function( text ) { + jQuery.globalEval( text ); + return text; + } + } +} ); + +// Handle cache's special case and crossDomain +jQuery.ajaxPrefilter( "script", function( s ) { + if ( s.cache === undefined ) { + s.cache = false; + } + if ( s.crossDomain ) { + s.type = "GET"; + } +} ); + +// Bind script tag hack transport +jQuery.ajaxTransport( "script", function( s ) { + + // This transport only deals with cross domain or forced-by-attrs requests + if ( s.crossDomain || s.scriptAttrs ) { + var script, callback; + return { + send: function( _, complete ) { + script = jQuery( " + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

all_lineage_prevalences(location, startswith)

+
+
+outbreak_data.all_lineage_prevalences(location, ndays=180, nday_threshold=10, other_threshold=0.05, other_exclude=None, cumulative=None, server='api.outbreak.info', auth=None, startswith=None)
+

Loads prevalence data from a location

+
+
Arguments:
+
location:
+

A string

+
+
other_threshold (Default:
+
    +

  1. Minimum prevalence threshold below which lineages must be accumulated under “Other”.

    2. +
+
+
nday_threshold (Default:
+
    +

  1. Minimum number of days in which the prevalence of a lineage must be below other_threshold to be accumulated under “Other”.

    2. +
+
+
ndays (Default:
+
    +

  1. The number of days before the current date to be used as a window to accumulate lineages under “Other”.

    2. +
+
+
other_exclude:
+

Comma separated lineages that are NOT to be included under “Other” even if the conditions specified by the three thresholds above are met.

+
+
cumulative:
+

(Default: false) If true return the cumulative prevalence.:startswith: A string; loads data for all lineages beginning with first letter(s) of name

+
+
return:
+

A pandas dataframe

+
+
+
+
+
+ +

Example usage:

+
#Find the prevalence all lineages in Argentina that begin with 'xbb.1'
+df = od.prevalence_by_location("ARG", startswith = 'xbb.1')
+print(df)
+
+
+
+
Output
+
             date  total_count  lineage_count  lineage  prevalence  \
+ 1454  2022-10-12            3              1    xbb.1    0.333333
+ 1455  2022-10-13            0              0    xbb.1    0.000000
+ 1456  2022-10-14            0              0    xbb.1    0.000000
+ 1457  2022-10-15            0              0    xbb.1    0.000000
+ 1458  2022-10-16            0              0    xbb.1    0.000000
+ ...          ...          ...            ...      ...         ...
+ 1673  2023-03-17            0              0  xbb.1.5    0.000000
+ 1674  2023-03-18            0              0  xbb.1.5    0.000000
+ 1675  2023-03-19            0              0  xbb.1.5    0.000000
+ 1676  2023-03-20            0              0  xbb.1.5    0.000000
+ 1677  2023-03-21            1              1  xbb.1.5    1.000000
+
+       prevalence_rolling
+ 1454            0.350000
+ 1455            0.179487
+ 1456            0.109375
+ 1457            0.065421
+ 1458            0.058577
+ ...                  ...
+ 1673            1.000000
+ 1674            1.000000
+ 1675            1.000000
+ 1676            1.000000
+ 1677            1.000000
+
+
+
+

[224 rows x 6 columns]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/auth_setup.html b/auth_setup.html new file mode 100644 index 0000000..04d42ca --- /dev/null +++ b/auth_setup.html @@ -0,0 +1,139 @@ + + + + + + + authenticate_new_user() — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

authenticate_new_user()

+
+
+authenticate_user.authenticate_new_user()
+

Authenticate a user for genomics API access. Required to complete for first time use.

+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/cases_by_location.html b/cases_by_location.html new file mode 100644 index 0000000..6ccaff2 --- /dev/null +++ b/cases_by_location.html @@ -0,0 +1,194 @@ + + + + + + + cases_by_location(location) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

cases_by_location(location)

+
+
+outbreak_data.cases_by_location(location, server='api.outbreak.info', auth=None, pull_smoothed=0)
+

Loads data from a location if input is a string, or from multiple locations +if location is a list of string locations. Since this API endpoint supports paging, collect_all is used to return all data.

+
+
Arguments:
+
location:
+

A string or list of strings, separate multiple locations by “,”

+
+
pull_smoothed:
+

For every value >= 0, returns 1000 obs. (paging)

+
+
return:
+

A pandas dataframe

+
+
+
+
+
+ +

Example usage:

+
#Get the number of SARS-CoV-2 cases in Colorado.
+df = outbreak_data.cases_by_location('USA_US-CO')
+print(df)
+
+
+
+
Output:
+
                              _id    _score    admin1   confirmed_numIncrease  \
+ 0     USA_Colorado_None2021-03-14  8.438688  Colorado                    505
+ 1     USA_Colorado_None2021-03-18  8.438688  Colorado                   1060
+ 2     USA_Colorado_None2021-03-20  8.438688  Colorado                    852
+ 3     USA_Colorado_None2021-03-26  8.438688  Colorado                   1184
+ 4     USA_Colorado_None2021-04-07  8.438688  Colorado                   1897
+ ...                           ...       ...       ...                    ...
+ 1116  USA_Colorado_None2022-06-22  8.397695  Colorado                   2226
+ 1117  USA_Colorado_None2022-06-29  8.397695  Colorado                   2402
+ 1118  USA_Colorado_None2022-07-09  8.397695  Colorado                   1348
+ 1119  USA_Colorado_None2022-07-14  8.397695  Colorado                   1924
+ 1120  USA_Colorado_None2022-07-16  8.397695  Colorado                   1231
+
+             date
+ 0     2021-03-14
+ 1     2021-03-18
+ 2     2021-03-20
+ 3     2021-03-26
+ 4     2021-04-07
+ ...          ...
+ 1116  2022-06-22
+ 1117  2022-06-29
+ 1118  2022-07-09
+ 1119  2022-07-14
+ 1120  2022-07-16
+
+
+
+

[1121 rows x 5 columns]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/collection_date.html b/collection_date.html new file mode 100644 index 0000000..06596f6 --- /dev/null +++ b/collection_date.html @@ -0,0 +1,169 @@ + + + + + + + collection_date(pango_lin, mutations=None, location=None) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • collection_date(pango_lin, mutations=None, location=None)
    • +
  • + View page source +
    • +
+
+
+
+
+ +
+

collection_date(pango_lin, mutations=None, location=None)

+
+
+outbreak_data.collection_date(pango_lin, mutations=None, location=None, server='api.outbreak.info')
+

Most recent collection date by location

+
+
Arguments:
+
pango_lin:
+

A string. (Required).

+
+
mutations:
+

(Optional). A string or list of strings. Comma separated list of mutations.

+
+
location:
+

(Optional). If not specified, return most recent date globally.

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +

Example usage:

+
df = od.collection_date('b.1.1.7', location='IND')
+print(df)
+
+
+
+
Output
+
                 Values
+ date        2021-11-26
+ date_count           2
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/cryptic_vars.html b/cryptic_vars.html new file mode 100644 index 0000000..9e90d87 --- /dev/null +++ b/cryptic_vars.html @@ -0,0 +1,205 @@ + + + + + + + Tracing Mutations Back to Lineage — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Tracing Mutations Back to Lineage

+

The Python Outbreak API can be queried in order to determine which lineages a mutation has been found in. After collecting a sample and determining what sequences are present, we may have a list of several SARS-CoV-2 mutations that we can immediately say are characteristic of a specific variant. However in some cases, we also may have a mutation that is relatively uncommon in most other samples. +For example, we can look at small data sample consisting of 10 mutations: (S:A67V, S:DEL69/70, S:E484A, S:N501Y, S:T572N, S:D614G, S:G142D N:S2Y, S:Q52R, E:L21F, S:G593D). We’ll want a way to find more details about any mutation collected, such as whether the mutation has been collected before, when, and where that mutation came from.

+

To start, the mutations_by_lineage() function allows us to look at the clinical prevalence of a mutation and see which lineage it most likely belongs to. Let’s try it for E:L21F:

+
# Perform authentication if you haven't already
+from outbreak_data import authenticate_user
+authenticate_user.authenticate_new_user()
+
+# Import outbreak_data package
+from outbreak_data import outbreak_data as od
+
+lin1 = od.mutations_by_lineage(mutation='E:L21F')
+print(lin1)
+
+
+
+
Output
+
          pangolin_lineage  lineage_count  mutation_count  proportion  \
+     0               ba.2        1228296             560    0.000456
+     1            b.1.1.7        1155169             844    0.000731
+     2             ba.1.1        1046121             268    0.000256
+     3               ay.4         861521             526    0.000611
+     4               ba.1         439838              49    0.000111
+     ...               ...            ...             ...         ...
+     400          ba.2.77             63              48    0.761905
+     401        ba.5.2.54             55               2    0.036364
+     402          b.1.616             39               3    0.076923
+     403        b.1.1.386             20               1    0.050000
+     404        b.1.1.400             20              20    1.000000
+
+          proportion_ci_lower  proportion_ci_upper
+     0               0.000419             0.000495
+     1               0.000683             0.000781
+     2               0.000227             0.000288
+     3               0.000560             0.000664
+     4               0.000083             0.000146
+     ...                   ...                  ...
+     400             0.646596             0.853783
+     401             0.007632             0.111568
+     402             0.022142             0.191265
+     403             0.005449             0.210819
+     404             0.883361             0.999976
+
+
+
+

[405 rows x 6 columns]

+

This mutation has clearly been seen before in some previous lineages. We might be able recognize that most of the mutations in our list have been detected in older variants, as well as Omicron. However, S:G593D is relatively uncommon in most other samples. We can easily find out where and when it was last detected:

+
>>>  lin2 = od.mutations_by_lineage(mutation='S:G593D')
+>>>  print(lin2)
+
+     pangolin_lineage  lineage_count  mutation_count  proportion  \
+ 0            xbb.1          28205               1    0.000035
+
+    proportion_ci_lower  proportion_ci_upper
+ 0             0.000004             0.000166
+
+
+>>>  last_seen = od.collection_date('xbb.1', 'S:G593D')
+>>>  print(last_seen)
+
+                Values
+ date        2022-12-12
+ date_count           1
+
+
+

According to our data, S:G593D has only been detected once in a single sequence belonging to the xbb.1 lineage. The last time it was collected was back on December 12, 2022.

+

Additionally mutations_by_lineage allows us to find out if there is a lineage where several mutations overlap. Selecting 7 of the mutations from our original list yields one lineage with all of these mutation characteristics:

+
>>> lin3 = od.mutations_by_lineage(mutation='S:A67V, S:DEL69/70, S:E484A, S:N501Y, S:T572N, S:D614G, S:G142D')
+>>> print(lin3)
+
+     pangolin_lineage  lineage_count  mutation_count  proportion  \
+   0          ba.1.19           4587               1    0.000218
+
+   proportion_ci_lower  proportion_ci_upper
+0             0.000024             0.001019
+
+
+

Here we see that the only lineage that contains all 7 mutations is ba.1.19.

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/daily_lag.html b/daily_lag.html new file mode 100644 index 0000000..332dae6 --- /dev/null +++ b/daily_lag.html @@ -0,0 +1,179 @@ + + + + + + + daily_lag(location=None) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

daily_lag(location=None)

+
+
+outbreak_data.daily_lag(location=None, server='api.outbreak.info')
+

Return the daily lag between collection and submission dates by location

+
+
Arguments:
+
location_id:
+

(Optional). If not specified, return lag globally.

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +

Example usage:

+
df = outbreak_data.daily_lag('LUX')
+print(df)
+
+
+
+
Output
+
              Key      Values             Key      Values             Key  \
+ 0  date_collected  2020-02-29  date_collected  2020-02-29  date_collected
+ 1  date_submitted  2020-03-07  date_submitted  2020-04-02  date_submitted
+ 2     total_count           1     total_count           1     total_count
+
+        Values             Key      Values             Key      Values  ...  \
+ 0  2020-03-05  date_collected  2020-03-06  date_collected  2020-03-07  ...
+ 1  2020-04-02  date_submitted  2020-04-02  date_submitted  2020-04-02  ...
+ 2           1     total_count           1     total_count           1  ...
+
+               Key      Values             Key      Values             Key  \
+ 0  date_collected  2023-04-28  date_collected  2023-04-29  date_collected
+ 1  date_submitted  2023-05-10  date_submitted  2023-05-10  date_submitted
+ 2     total_count          20     total_count          11     total_count
+
+        Values             Key      Values             Key      Values
+ 0  2023-04-30  date_collected  2023-05-01  date_collected  2023-05-02
+ 1  2023-05-10  date_submitted  2023-05-10  date_submitted  2023-05-10
+ 2           1     total_count           5     total_count           2
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/daily_prev.html b/daily_prev.html new file mode 100644 index 0000000..8c1df40 --- /dev/null +++ b/daily_prev.html @@ -0,0 +1,308 @@ + + + + + + + + + + + daily_prev(pango_lin, location, mutations, cumulative) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +
+ + + + + +
+
+ Join us on GitHub +
+ + +
+ + + + + + + + + + + + + + + + + + + +
+ +
    + +
  • »
    • + +
  • daily_prev(pango_lin, location, mutations, cumulative)
    • + + +
  • + + + View page source + + +
    • + +
+ + +
+
+
+
+ +
+

daily_prev(pango_lin, location, mutations, cumulative)

+

Example usage:

+
    +

  1. Get the daily prevalence of lineage ‘BA.2’ in India since first detection:

    +
    df1 = od.daily_prev('ba.2', "IND")
+print(df1)
+
    +
    +
    2. +
+
+
Output
+
             date  total_count  lineage_count  total_count_rolling  \
+ 0     2020-08-01           39              1            29.000000
+ 1     2020-08-02          100              0            41.285714
+ 2     2020-08-03           38              0            42.000000
+ 3     2020-08-04           20              0            42.285714
+ 4     2020-08-05           26              0            36.000000
+ ...          ...          ...            ...                  ...
+ 1017  2023-05-15            2              0             5.857143
+ 1018  2023-05-16            3              0             5.142857
+ 1019  2023-05-17            3              0             3.285714
+ 1020  2023-05-18            2              0             3.142857
+ 1021  2023-05-20            1              0             2.000000
+
+       lineage_count_rolling  proportion  proportion_ci_lower  \
+ 0                  0.142857    0.004926             0.000017
+ 1                  0.142857    0.003460             0.000012
+ 2                  0.142857    0.003401             0.000012
+ 3                  0.142857    0.003378             0.000012
+ 4                  0.142857    0.003968             0.000014
+ ...                     ...         ...                  ...
+ 1017               0.000000    0.000000             0.000078
+ 1018               0.000000    0.000000             0.000093
+ 1019               0.000000    0.000000             0.000151
+ 1020               0.000000    0.000000             0.000151
+ 1021               0.000000    0.000000             0.000217
+
+       proportion_ci_upper
+ 0                0.082286
+ 1                0.059076
+ 2                0.057719
+ 3                0.057719
+ 4                0.066944
+ ...                   ...
+ 1017             0.330389
+ 1018             0.379377
+ 1019             0.535583
+ 1020             0.535583
+ 1021             0.666822
+
+
+
+
    +

  1. Get a cumulative summary of information regarding ‘BA.2’ in India:

    +
    df2 = od.daily_prev('ba.2', "IND", cumulative = True)
+print(df2)
+
    +
    +
    2. +
+
+
Output
+
                        Values
+ first_detected     2020-08-01
+ global_prevalence    0.109641
+ last_detected      2023-04-26
+ lineage_count           25561
+ total_count            233134
+
+
+
+
+ + +
+ +
+ +
+
+ +
+ +
+ + + + + + + + + + + \ No newline at end of file diff --git a/epidem_analysis.html b/epidem_analysis.html new file mode 100644 index 0000000..f9000e5 --- /dev/null +++ b/epidem_analysis.html @@ -0,0 +1,214 @@ + + + + + + + Working with epidemiological data — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Working with epidemiological data

+

The outbreak_data package contains endpoints that return epidemiological data on SARS-CoV-2. We can then visualize how SARS-CoV-2 is affecting countries around the world (with the help of one of the many plotting packages available for Python).

+

For example, we can look at the pattern of infection counts in California during a specific point in time:

+
# Perform authentication
+from outbreak_data import authenticate_user
+authenticate_user.authenticate_new_user()
+
+# Import outbreak_data package
+from outbreak_data import outbreak_data as od
+import pandas as pd
+
+# Get the number of increased cases from the previous day in California
+counts_ca = od.cases_by_location('USA_US-CA')
+# Formatting for graph
+counts_ca= counts_ca.rename(columns={"admin1": "location"})
+# Sort info by date and search within a date range
+counts_ca = counts_ca.sort_values(by = "date")
+counts_ca = counts_ca.loc[counts_ca["date"].between("2021-05-15", "2021-08-15")]
+print(counts_ca)
+
+#Import visual package of choice
+import altair as alt
+
+#Graph!
+alt.Chart(xbb_mutations, title = "Daily ORF1a:K47R AND S:T19I Prevalence of Lineage XBB").mark_line().encode(
+x='date:T',
+y=alt.Y('proportion (%):Q'),
+color = 'mutations:N')
+
+
+
+
Output
+
      _id    _score    location  \
+ 621  USA_California_None2021-05-15  8.418888  California
+ 622  USA_California_None2021-05-16  8.418888  California
+ 623  USA_California_None2021-05-17  8.418888  California
+ 624  USA_California_None2021-05-18  8.418888  California
+ 625  USA_California_None2021-05-19  8.418888  California
+ ..                             ...       ...         ...
+ 166  USA_California_None2021-08-11  8.419768  California
+ 644  USA_California_None2021-08-12  8.418888  California
+ 413  USA_California_None2021-08-13  8.418888  California
+ 167  USA_California_None2021-08-14  8.419768  California
+ 414  USA_California_None2021-08-15  8.418888  California
+
+      confirmed_numIncrease        date
+ 621                   1504  2021-05-15
+ 622                   1087  2021-05-16
+ 623                    793  2021-05-17
+ 624                   1054  2021-05-18
+ 625                   1400  2021-05-19
+ ..                     ...         ...
+ 166                  11164  2021-08-11
+ 644                  14356  2021-08-12
+ 413                  15707  2021-08-13
+ 167                  13100  2021-08-14
+ 414                  10744  2021-08-15
+ [93 rows x 5 columns]
+
+
+
+_images/ca_cases.png +

We can also do the same analysis over multiple locations and visualize them all at once:

+
counts_ca = od.cases_by_location('USA_US-NY')
+counts_ny = od.cases_by_location('USA_US-TX')
+counts_fl = od.cases_by_location('USA_US-LA')
+counts_wa = od.cases_by_location('USA_US-FL')
+
+state_count = pd.concat([counts_ca, counts_ny, counts_fl, counts_wa])
+state_count = state_count.rename(columns={"admin1": "location"})
+state_count = state_count.sort_values(by = "date")
+state_count = state_count.loc[state_count["date"].between("2020-10-15", "2021-01-15")]
+
+#Graph it!
+alt.Chart(state_count, title = " 90 Day SARS-COV-2 Case Count Increase in Four States").mark_line().encode(
+x='date:T',
+y=alt.Y('confirmed_numIncrease:Q'),
+color = 'location:N')
+
+
+_images/multi_state_cases.png +
+

Note

+

The Vega-Altair visualization package is used for demonstration purposes. However, any Python visual package can be used to create graphical representations of the data.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genindex.html b/genindex.html new file mode 100644 index 0000000..1fd2514 --- /dev/null +++ b/genindex.html @@ -0,0 +1,245 @@ + + + + + + Index — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Index
    • +
  • +
    • +
+
+
+
+
+ + +

Index

+ +
+ A + | C + | D + | G + | L + | M + | P + | S + | W + +
+

A

+ + + +
+ +

C

+ + + +
+ +

D

+ + +
+ +

G

+ + + +
+ +

L

+ + + +
+ +

M

+ + + +
+ +

P

+ + +
+ +

S

+ + + +
+ +

W

+ + + +
+ + + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/genomic_analysis.html b/genomic_analysis.html new file mode 100644 index 0000000..c44e5c5 --- /dev/null +++ b/genomic_analysis.html @@ -0,0 +1,497 @@ + + + + + + + + + + + Genomic Analysis — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +
+ + + + + +
+
+ Join us on GitHub +
+ + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + +
+
+
+
+ +
+

Genomic Analysis

+

The outbreak_data package has contains multiple tools that can collect the relevant genomic information on SARS-CoV-2. Using a combination of these endpoints will allow you to get the information on variants of concern (VoC) and the current mutations to conduct your own multi-level genomic analysis on SARS-CoV-2. On this page, you’ll find a few example workflows that demonstrate data manipulation and visualization steps to track the progression of SARS-CoV-2.

+

Here is an example workflow that allows the user to manipulate the data to find all the XBB lineages prevalent in India within a 1-year timeframe:

+
# Perform authentication if you haven't already
+from outbreak_data import authenticate_user
+authenticate_user.authenticate_new_user()
+
+# Import outbreak_data package
+from outbreak_data import outbreak_data as od
+
+# Get the prevalence of all circulating XBB lineages in India
+data = od.prevalence_by_location("IND", startswith = 'xbb')
+# multiply prevalence values by 100% for scale
+data['prevalence_rolling'] = data['prevalence_rolling'].apply(lambda x: x*100)
+# Search for data based on date range
+data = data.sort_values(by="date")
+data = data.loc[data["date"].between("2020-09-12", "2022-03-31")]
+
+## Use the visual package of your choice to create an area graph using your data
+import altair as alt
+
+# Graph of results
+alt.Chart(data, title = "Lineage Prevalence in India").mark_area().encode(
+x='date:T',
+y=alt.Y('prevalence_rolling:Q'),
+color = 'lineage:N')
+
+
+
+
Output:
+
            date  total_count  lineage_count     lineage  prevalence  \
+ 3014 2022-09-12            0              0    xbb.1.16    0.000000
+ 3781 2022-09-12            0              0     xbb.2.3    0.000000
+ 2593 2022-09-12          152              2       xbb.1    0.013158
+ 3782 2022-09-13            0              0     xbb.2.3    0.000000
+ 3015 2022-09-13            0              0    xbb.1.16    0.000000
+ ...         ...          ...            ...         ...         ...
+ 4086 2023-03-31          196              2   xbb.2.3.2    0.010204
+ 3322 2023-03-31          196             29  xbb.1.16.1    0.147959
+ 2793 2023-03-31          196              1       xbb.1    0.005102
+ 3381 2023-03-31          196              7  xbb.1.16.2    0.035714
+ 3981 2023-03-31          196             15     xbb.2.3    0.076531
+
+      prevalence_rolling
+ 3014            0.000000
+ 3781            0.000000
+ 2593            0.003451
+ 3782            0.000000
+ 3015            0.000000
+ ...                  ...
+ 4086            0.031184
+ 3322            0.144578
+ 2793            0.014174
+ 3381            0.045358
+ 3981            0.084337
+[985 rows x 6 columns]
+
+
+
+_images/prev_visual.png +
+

Note

+

The Vega-Altair visualization package is used for demonstration purposes. However, any Python visual package can be used to create graphical representations of the data.

+
+

Lineage_Mutations Heatmap

+

A basic but important question: how do we define a lineage? What mutations consistently appear in most sequences within a lineage? We could start by plotting some of the characteristic mutations of XBB occurring in 80% of sequences. Even better, we can do this for mulitple related lineages and compare them using a heatmap:

+
# Collecting 15 characteristic mutations and their prevalences for each variant
+lin0 = od.lineage_mutations("xbb", freq = 0.80)
+lin0["lineage"] = "xbb"
+lin0 = lin0.iloc[:15]
+
+lin1 = od.lineage_mutations("xbb.1", freq = 0.80)
+lin1["lineage"] = "xbb.1"
+lin1 = lin1.iloc[:15]
+
+lin2 = od.lineage_mutations("xbb.1.5", freq = 0.80)
+lin2["lineage"] = "xbb.1.5"
+lin2 = lin2.iloc[:15]
+
+lin3 = od.lineage_mutations("xbb.1.16", freq = 0.80)
+lin3["lineage"] = "xbb.1.16"
+lin3 = lin3.iloc[:15]
+
+lin4 = od.lineage_mutations("xbb.1.9", freq = 0.80)
+lin4["lineage"] = "xbb.1.9"
+lin4 = lin4.iloc[:15]
+
+lin5 = od.lineage_mutations("xbb.2.3", freq = 0.80)
+lin5["lineage"] = "xbb.2.3"
+lin5 = lin5.iloc[:15]
+
+# Link each of the findings together for plotting
+df = pd.concat([lin0, lin1, lin2, lin3, lin4, lin5])
+df["prevalence"] = df["prevalence"].apply(lambda x: x*100)
+df= df.rename(columns={'prevalence': 'prevalence %'})
+
+# Plot mutation heatmap
+import altair as alt
+
+alt.Chart(df).mark_rect().encode(
+    x = "mutation:N",
+    y = "lineage:N",
+    color = 'prevalence %:Q')
+
+
+
+
Output
+
         mutation  mutation_count  lineage_count  lineage   gene ref_aa alt_aa  \
+ 0      orf6:d61l            4198           4423      xbb   ORF6      D      L
+ 1         s:l24s            3919           4423      xbb      S      L      S
+ 2        n:r203k            4378           4423      xbb      N      R      K
+ 3        s:g339h            4054           4423      xbb      S      G      H
+ 4        s:v445p            3643           4423      xbb      S      V      P
+ ...           ...             ...            ...      ...    ...    ...    ...
+ 10  orf1a:p3395h            3263           3279  xbb.2.3  ORF1a      P      H
+ 11       s:n969k            3261           3279  xbb.2.3      S      N      K
+ 12  orf1a:g1307s            3257           3279  xbb.2.3  ORF1a      G      S
+ 13       s:d614g            3257           3279  xbb.2.3      S      D      G
+ 14       s:q954h            3257           3279  xbb.2.3      S      Q      H
+
+     codon_num codon_end          type  prevalence % change_length_nt
+ 0          61      None  substitution     94.912955             None
+ 1          24      None  substitution     88.605019             None
+ 2         203      None  substitution     98.982591             None
+ 3         339      None  substitution     91.657246             None
+ 4         445      None  substitution     82.364911             None
+ ...        ...       ...           ...           ...              ...
+ 10       3395      None  substitution     99.512046             None
+ 11        969      None  substitution     99.451052             None
+ 12       1307      None  substitution     99.329064             None
+ 13        614      None  substitution     99.329064             None
+ 14        954      None  substitution     99.329064             None
+
+
+
+

[90 rows x 12 columns]

+_images/mut_by_lin.png +

Comparing Lineages

+

To better understand the evolution of SARS-CoV-2, we may also want to know what mutations are shared between different viral lineages and how many shared mutations there are.

+

For this example we’ll look at three different lineages: B.1.1.7, P.1, and B.1.1.529. First, let’s get an idea of which mutations are shared between all three lineages:

+
lin1 = od.lineage_mutations("b.1.1.7")
+lin1["lineage"] = "b.1.1.7"
+
+lin2 = od.lineage_mutations("P.1")
+lin2["lineage"] = "P.1"
+
+lin3 = od.lineage_mutations("b.1.1.529")
+lin3["lineage"] = "b.1.1.529"
+
+#Finding intersections
+
+#Created an optional but convenient intersecting function
+def intersect(lst1, lst2):
+    return set(lst1).intersection(lst2)
+
+a = set(lin1['mutation'])
+b = set(lin2['mutation'])
+c = set(lin3['mutation'])
+
+m12 = intersect(a, b)
+m13 = intersect(a, c)
+m23 = intersect(b, c)
+m123 = intersect(m12, c)
+
+print('Set 1.2:', m12)
+print('Set 1.3:', m13)
+print('Set 2.3:' , m23)
+print('Set 1.2.3:', m123)
+
+
+
+
Output
+
 Set 1.2: {'orf1b:p314l', 'orf8:s84l', 'orf1a:del3675/3677', 'n:r203k', 's:d614g', 's:n501y', 'n:g204r'}
+ Set 1.3: {'s:p681h', 'orf1b:p314l', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'}
+ Set 2.3: {'orf1b:p314l', 's:h655y', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'}
+ Set 1.2.3: {'orf1b:p314l', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'}
+
+
+
+

Finally, we can make a visual based on our findings and create a Venn diagram of our results:

+
# Import libraries for venn diagram visual
+from matplotlib_venn import venn3, venn3_circles
+from matplotlib import pyplot as plt
+
+# Using matplotlib_venn to make venn diagram with custom visuals
+ ## The venn diagram package used here automatically determines the number
+ ## of intersecting values and plots accordingly
+
+vd3 = venn3([a, b, c], set_labels = ('Alpha/B.1.1.7', 'Gamma/P.1', 'Omicron/B.1.1.529'), set_colors=('#c4e6ff', '#F4ACB7','#9D8189'),
+ alpha = 0.8)
+c = venn3_circles([a, b, c,], linestyle = '-.', linewidth=2, color='grey')
+for text in vd3.set_labels:
+ text.set_fontsize(16);
+for text in vd3.subset_labels:
+ text.set_fontsize(16)
+plt.title('Number of Overlapping Mutations in 3 Variants',fontname ='Helvetica',fontweight ='bold',fontsize = 18,
+ pad = 30,backgroundcolor ='#cbe7e3',color ='black', style ='normal');
+c[0].set_lw(7.0)
+c[0].set_ls(':')
+plt.show()
+
+
+_images/compare.png +

We can see that the graph matches the number of intersecting mutations that we previously saw, given that the venn diagram also takes into account unique values for each set.

+
+

Note

+

Please see the matplotlib venn diagram documentation and this article for more info on how to create these graphs.

+
+

Finding the Most Prevalent Lineages

+

If we wanted to determine and plot the top four most prevalent lineages in India, we can make a few queries and use a few simple commands to create a table that shows us what these lineages are:

+
data=od.prevalence_by_location("IND")
+most_prev = data.groupby('lineage').apply(max) # Finds the lineages with the most hits
+most_prev = most_prev.mask(most_prev == '').dropna(how = 'any') # Drop any unknowns
+most_prev = most_prev.iloc[:4]
+print(most_prev)
+
+
+
+
Output
+
                  date  total_count  lineage_count    lineage  prevalence  \
+ lineage
+ ba.2       2023-04-20         5668           1445       ba.2    0.822785
+ ba.2.10.1  2023-04-19         5668             93  ba.2.10.1    0.285714
+ bq.1.1     2023-03-27          402              7     bq.1.1    0.428571
+ ch.1.1     2023-02-13          119              4     ch.1.1    0.400000
+
+            prevalence_rolling
+ lineage
+ ba.2                 0.677541
+ ba.2.10.1            0.095541
+ bq.1.1               0.156863
+ ch.1.1               0.066667
+
+
+
+

Next we’ll collect the prevalence data on each of the four lineages:

+
# Retrieve the official data on the prevalences of these lineages using `daily_prev()`
+d1 = od.daily_prev('ba.2', "IND")
+d2 = od.daily_prev('ba.2.10.1', "IND")
+d3 = od.daily_prev('bq.1.1', "IND")
+d4 = od.daily_prev( 'ch.1.1', "IND")
+
+# Formatting for creating the graph
+d1['lineage'] = 'ba.2'
+d2['lineage'] = 'ba.2.10.1'
+d3['lineage'] = 'bq.1.1'
+d4['lineage'] = 'ch.1.1'
+
+# Group together data from each lineage
+data = pd.concat([d1, d2, d3, d4])
+data = data.rename(columns = {'proportion': 'proportion (%)'})
+
+#Pick a date range to analyze
+data = data.sort_values(by="date")
+data = data.loc[data["date"].between("2022-09-12", "2023-03-31")]
+# Increase prevalence by 100%
+data['proportion'] = data['proportion'].apply(lambda x: x*100)
+
+#Graph using preferred visual package
+import altair as alt
+alt.Chart(data, title = "Top 4 Most Prevalent Lineages in India").mark_area().encode(
+x='date:T',
+y=alt.Y('proportion (%):Q'),
+color = 'lineage:N')
+
+
+_images/top4.png +
+ + +
+ +
+ +
+
+ +
+ +
+ + + + + + + + + + + \ No newline at end of file diff --git a/global_prevalence.html b/global_prevalence.html new file mode 100644 index 0000000..51b7b9e --- /dev/null +++ b/global_prevalence.html @@ -0,0 +1,209 @@ + + + + + + + global_prevalence(pango_lin, mutations, cumulative, lineage_crumbs=False) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • global_prevalence(pango_lin, mutations, cumulative, lineage_crumbs=False)
    • +
  • + View page source +
    • +
+
+
+
+
+ +
+

global_prevalence(pango_lin, mutations, cumulative, lineage_crumbs=False)

+
+
+outbreak_data.global_prevalence(pango_lin, mutations=None, cumulative=None, server='api.outbreak.info')
+

Returns the global daily prevalence of a PANGO lineage

+
+
Arguments:
+
pangolin_lineage:
+

(Required).

+
+
mutations:
+

(Optional). Comma separated list of mutations.

+
+
cumulative:
+

(Optional). If true returns the cumulative global prevalence since the first day of detection.

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +

Example: Get global info on lineage ‘XBB’:

+
df = outbreak_data.global_prevalence('xbb')
+print(df)
+
+
+
+
Output:
+
            date  total_count  lineage_count  total_count_rolling  \
+ 0    2021-06-29        15453              2         10772.428571
+ 1    2021-06-30        13101              0         11060.571429
+ 2    2021-07-01        13088              0         11495.000000
+ 3    2021-07-02        11562              0         11890.571429
+ 4    2021-07-03         8310              0         11845.571429
+ ..          ...          ...            ...                  ...
+ 713  2023-06-12           27              0           112.428571
+ 714  2023-06-13            8              0            61.714286
+ 715  2023-06-14            1              0            36.000000
+ 716  2023-06-15            1              0            25.285714
+ 717  2023-06-17            1              0             8.000000
+
+      lineage_count_rolling  proportion  proportion_ci_lower  \
+ 0                 0.285714    0.000027         4.558329e-08
+ 1                 0.285714    0.000026         4.439232e-08
+ 2                 0.285714    0.000025         4.271630e-08
+ 3                 0.285714    0.000024         4.129377e-08
+ 4                 0.285714    0.000024         4.145063e-08
+ ..                     ...         ...                  ...
+ 713               0.142857    0.001271         4.374452e-06
+ 714               0.000000    0.000000         7.888011e-06
+ 715               0.000000    0.000000         1.354537e-05
+ 716               0.000000    0.000000         1.944577e-05
+ 717               0.000000    0.000000         5.949030e-05
+
+      proportion_ci_upper
+ 0               0.000233
+ 1               0.000227
+ 2               0.000218
+ 3               0.000211
+ 4               0.000212
+ ..                   ...
+ 713             0.022129
+ 714             0.039548
+ 715             0.066944
+ 716             0.094683
+ 717             0.262217
+
+
+
+

[718 rows x 8 columns]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/growth_rates.html b/growth_rates.html new file mode 100644 index 0000000..caa116f --- /dev/null +++ b/growth_rates.html @@ -0,0 +1,153 @@ + + + + + + + growth_rates(lineage, location) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

growth_rates(lineage, location)

+
+
+outbreak_data.growth_rates(lineage, location='Global')
+

Returns the growth rate score for a given lineage in a given location.

+
+
Arguments:
+
lineage:
+

(Required) A string.

+
+
location:
+

(Required. Default: ‘Global’) A list or string. Separate multiple locations with “,”

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/id_lookup.html b/id_lookup.html new file mode 100644 index 0000000..0b5cd41 --- /dev/null +++ b/id_lookup.html @@ -0,0 +1,228 @@ + + + + + + + + + + + id_lookup(locations, max_results = 10, table = False) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +
+ + + + + +
+
+ Join us on GitHub +
+ + +
+ + + + + + + + + + + + + + + + + + + +
+ +
    + +
  • »
    • + +
  • id_lookup(locations, max_results = 10, table = False)
    • + + +
  • + + + View page source + + +
    • + +
+ + +
+
+
+
+ +
+

id_lookup(locations, max_results = 10, table = False)

+
+ + +
+ +
+ +
+
+ +
+ +
+ + + + + + + + + + + \ No newline at end of file diff --git a/index.html b/index.html new file mode 100644 index 0000000..cb08f97 --- /dev/null +++ b/index.html @@ -0,0 +1,262 @@ + + + + + + + Welcome to the Python Outbreak.info package docs! — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Welcome to the Python Outbreak.info package docs!

+

Here you can find information on the functions you will use to collect and analyze SARS-COV-2 data from the Outbreak.info API. +Our package pulls data from the Outbreak.info API and is reflected on our Outbreak.info web interface

+
+

Installation

+

We recommend installing the package via pip using:

+

pip install python-outbreak-info

+

Alternatively, the package can be directly installed from source via pip:

+

pip install git+https://github.com/outbreak-info/python-outbreak-info.git

+
+
+

Getting Started

+

The Python Outbreak.info package contains key functions for accessing genomic and epidemiological data for SARS-CoV-2. Access to genomic data requires logging in using GISAID credentials to generate an API key, using the authenticate_new_user() function. To perform authentication, you’ll need to first run

+
from outbreak_data import authenticate_user
+authenticate_user.authenticate_new_user()
+
+
+

and then you should be able access all of the functionality of the package. Most of the rest of the tools are available within the outbreak_data component of the package. For example:

+
from outbreak_data import outbreak_data
+lin_list = ['B.1.1.7','B.1.351','B.1.617.2']
+# request lineages occurring with minimum frequency of 0.05 (5%)
+df = outbreak_data.lineage_mutations(lin_list,freq=0.05)
+# filter mutations and sort by codon number
+df = df[df['gene']=='S'].sort_values(by='codon_num')
+
+
+

For location-specific analyses, users will need to supply the appropriate location code corresponding to their location of interest. To do this, we provide an ID lookup tool kit via the outbreak_tools part of the package. An example lookup should look like:

+
from outbreak_tools import outbreak_tools
+location_list = outbreak_tools.id_lookup(['Illinois','South Africa','Chile'])
+# which returns ['USA_US-IL', 'ZAF', 'CHL']
+
+
+
+

Note

+

This project is under active development.

+
+
+
+

Core Outbreak Data Tools

+
+ +
+
+
+

Example analyses:

+
+ +
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/lineage_by_sub_admin.html b/lineage_by_sub_admin.html new file mode 100644 index 0000000..ddc076a --- /dev/null +++ b/lineage_by_sub_admin.html @@ -0,0 +1,182 @@ + + + + + + + lineage_by_sub_admin(pango_lin, mutations, location, ndays=0, detected) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • lineage_by_sub_admin(pango_lin, mutations, location, ndays=0, detected)
    • +
  • + View page source +
    • +
+
+
+
+
+ +
+

lineage_by_sub_admin(pango_lin, mutations, location, ndays=0, detected)

+
+
+outbreak_data.lineage_by_sub_admin(pango_lin, mutations=None, location=None, ndays=0, detected=None, server='api.outbreak.info')
+

Cumulative prevalence of a PANGO lineage by the immediate admin level of a location

+

Arguments: +:pangolin_lineage: (Required). A list or string. List of lineages separated by , +:mutations: (Optional). A string or list of strings. Uses AND logic. +:location_id: (Optional). A string. If not specified, returns cumulative prevalence at the country level globally. +:ndays: (Optional). An integer. Specify number of days from current date to calculative cumuative counts. If not specified, there is no limit on the window. +:detected: (Optional). If true returns only if at least found in location +:return: A pandas dataframe.

+
+ +

Example usage:

+
df = od.lineage_by_sub_admin('xbb.1.15', location='FRA')
+print(df)
+
+
+
+
Output:
+
        date              name          id          total_count  lineage_count  \
+ 0  2023-06-04                      FRA_FR-none          3              0
+ 1  2023-05-31          Bretagne    FRA_FR-BT            2              0
+ 2  2023-05-22             Corse    FRA_FR-CE            1              0
+ 3  2023-05-30         Grand Est    FRA_FR-AO           68              0
+ 4  2023-06-04         Normandie    FRA_FR-ND            2              0
+ 5  2023-06-01         Occitanie    FRA_FR-LP            2              0
+ 6  2023-05-30  Pays de la Loire    FRA_FR-PL           22              0
+
+    cum_total_count  cum_lineage_count  proportion  proportion_ci_lower  \
+ 0           406320                 10    0.000025         1.265376e-05
+ 1            22070                  1    0.000045         4.888926e-06
+ 2             2007                  0    0.000000         2.446305e-07
+ 3            43954                  1    0.000023         2.454796e-06
+ 4            19479                  0    0.000000         2.520808e-08
+ 5            57933                  0    0.000000         8.475868e-09
+ 6            24556                  0    0.000000         1.999632e-08
+
+    proportion_ci_upper
+ 0             0.000044
+ 1             0.000212
+ 2             0.001251
+ 3             0.000106
+ 4             0.000129
+ 5             0.000043
+ 6             0.000102
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/lineage_mutations.html b/lineage_mutations.html new file mode 100644 index 0000000..3dd7456 --- /dev/null +++ b/lineage_mutations.html @@ -0,0 +1,332 @@ + + + + + + + lineage_mutations(pango_lin, mutation, freq) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

lineage_mutations(pango_lin, mutation, freq)

+
+
+outbreak_data.lineage_mutations(pango_lin=None, lineage_crumbs=False, mutations=None, freq=0.8, server='api.outbreak.info', auth=None)
+

Retrieves data from all mutations in a specified lineage above a frequency threshold. +- Use ‘OR’ in a string to return overlapping mutations in multiple lineages: ‘BA.2 OR BA.1’

+
+
+
Arguments:
+
pango_lin:
+

A string; loads data for all mutations in a specified PANGO lineage

+
+
lineage_crumbs:
+

If true returns data for descendant lineages of pango_lin. Include the wildcard ‘*’ in string to return info on all related lineages.

+
+
mutations:
+

A string; loads mutation data for the specified sequence under the specified PANGO lineage

+
+
freq:
+

A number between 0 and 1 specifying the frequency threshold above which to return mutations (default = 0.8)

+
+
return:
+

A pandas dataframe

+
+
+
+
+
+
+ +

Example usage:

+
    +

  1. Get a list of all mutations and relevant data associated with the variant ‘B.1.1.7’:

    +
    df = outbreak_data.lineage_mutations('b.1.1.7')
+print(df)
+
    +
    +
    2. +
+
+
Output:
+
               mutation  mutation_count  lineage_count  lineage   gene  \
+ 0                n:d3l         1133368        1154337  b.1.1.7      N
+ 1              n:r203k         1131899        1154337  b.1.1.7      N
+ 2              s:d614g         1150796        1154337  b.1.1.7      S
+ 3         orf1a:t1001i         1149579        1154337  b.1.1.7  ORF1a
+ 4            orf8:s84l         1148665        1154337  b.1.1.7   ORF8
+ 5              s:a570d         1147678        1154337  b.1.1.7      S
+ 6              s:p681h         1147591        1154337  b.1.1.7      S
+ 7          orf1b:p314l         1147331        1154337  b.1.1.7  ORF1b
+ 8             s:d1118h         1147009        1154337  b.1.1.7      S
+ 9         orf1a:a1708d         1146288        1154337  b.1.1.7  ORF1a
+ 10           orf8:y73c         1144041        1154337  b.1.1.7   ORF8
+ 11             s:s982a         1142512        1154337  b.1.1.7      S
+ 12           orf8:q27*         1142465        1154337  b.1.1.7   ORF8
+ 13             s:t716i         1142087        1154337  b.1.1.7      S
+ 14             n:s235f         1141424        1154337  b.1.1.7      N
+ 15           orf8:r52i         1138388        1154337  b.1.1.7   ORF8
+ 16             s:n501y         1129018        1154337  b.1.1.7      S
+ 17        orf1a:i2230t         1127643        1154337  b.1.1.7  ORF1a
+ 18  orf1a:del3675/3677         1115708        1154337  b.1.1.7  ORF1a
+ 19          s:del69/70         1114288        1154337  b.1.1.7      S
+ 20        s:del144/144         1093432        1154337  b.1.1.7      S
+ 21             n:g204r         1050444        1154337  b.1.1.7      N
+
+                 ref_aa        alt_aa  codon_num codon_end          type  \
+ 0                    D             L          3      None  substitution
+ 1                    R             K        203      None  substitution
+ 2                    D             G        614      None  substitution
+ 3                    T             I       1001      None  substitution
+ 4                    S             L         84      None  substitution
+ 5                    A             D        570      None  substitution
+ 6                    P             H        681      None  substitution
+ 7                    P             L        314      None  substitution
+ 8                    D             H       1118      None  substitution
+ 9                    A             D       1708      None  substitution
+ 10                   Y             C         73      None  substitution
+ 11                   S             A        982      None  substitution
+ 12                   Q             *         27      None  substitution
+ 13                   T             I        716      None  substitution
+ 14                   S             F        235      None  substitution
+ 15                   R             I         52      None  substitution
+ 16                   N             Y        501      None  substitution
+ 17                   I             T       2230      None  substitution
+ 18  ORF1A:DEL3675/3677  DEL3675/3677       3675    3677.0      deletion
+ 19          S:DEL69/70      DEL69/70         69      70.0      deletion
+ 20        S:DEL144/144    DEL144/144        144     144.0      deletion
+ 21                   G             R        204      None  substitution
+
+     prevalence change_length_nt
+ 0     0.981835             None
+ 1     0.980562             None
+ 2     0.996932             None
+ 3     0.995878             None
+ 4     0.995086             None
+ 5     0.994231             None
+ 6     0.994156             None
+ 7     0.993931             None
+ 8     0.993652             None
+ 9     0.993027             None
+ 10    0.991081             None
+ 11    0.989756             None
+ 12    0.989715             None
+ 13    0.989388             None
+ 14    0.988813             None
+ 15    0.986183             None
+ 16    0.978066             None
+ 17    0.976875             None
+ 18    0.966536              9.0
+ 19    0.965306              6.0
+ 20    0.947238              3.0
+ 21    0.909998             None
+
+
+
+
    +

  1. Mutiple queries for lineages and mutations can be separated by “,”:

    +
    #Find mutation information for B.1.1.7, P.1, and XBB.1.5
+df = outbreak_data_lineage_mutations('b.1.1.7, p.1, xbb.1.5')
+print(df)
+
    +
    +
    2. +
+
+
Output
+
         mutation  mutation_count  lineage_count  lineage   gene        ref_aa  \
+ 0          n:d3l         1133368        1154337  b.1.1.7      N             D
+ 1        n:r203k         1131899        1154337  b.1.1.7      N             R
+ 2        s:d614g         1150796        1154337  b.1.1.7      S             D
+ 3   orf1a:t1001i         1149579        1154337  b.1.1.7  ORF1a             T
+ 4      orf8:s84l         1148665        1154337  b.1.1.7   ORF8             S
+ ..           ...             ...            ...      ...    ...           ...
+ 63       s:g446s          156244         167128  xbb.1.5      S             G
+ 64  s:del144/144          154766         167128  xbb.1.5      S  S:DEL144/144
+ 65       s:h146q          153308         167128  xbb.1.5      S             H
+ 66       s:r408s          152365         167128  xbb.1.5      S             R
+ 67       s:k417n          147604         167128  xbb.1.5      S             K
+
+         alt_aa  codon_num codon_end          type  prevalence change_length_nt
+ 0            L          3      None  substitution    0.981835             None
+ 1            K        203      None  substitution    0.980562             None
+ 2            G        614      None  substitution    0.996932             None
+ 3            I       1001      None  substitution    0.995878             None
+ 4            L         84      None  substitution    0.995086             None
+ ..         ...        ...       ...           ...         ...              ...
+ 63           S        446      None  substitution    0.934876             None
+ 64  DEL144/144        144     144.0      deletion    0.926033              3.0
+ 65           Q        146      None  substitution    0.917309             None
+ 66           S        408      None  substitution    0.911667             None
+ 67           N        417      None  substitution    0.883179             None
+
+
+
+

[113 rows x 12 columns]

+
    +

  1. Use ‘OR’ in a string to return overlapping mutations in multiple lineages:

    +
    df = outbreak_data.lineage_mutations('ba.2 OR xbb.1.5')
+print(df)
+
    +
    +
    2. +
+
+
Output
+
              mutation  mutation_count  lineage_count         lineage   gene  \
+ 0             n:r203k          237984         243206  P.1 OR xbb.1.5      N
+ 1             s:d614g          242522         243206  P.1 OR xbb.1.5      S
+ 2         orf1b:p314l          242226         243206  P.1 OR xbb.1.5  ORF1b
+ 3             s:h655y          241765         243206  P.1 OR xbb.1.5      S
+ 4           orf8:s84l          240116         243206  P.1 OR xbb.1.5   ORF8
+ 5             n:g204r          238101         243206  P.1 OR xbb.1.5      N
+ 6             s:n501y          235654         243206  P.1 OR xbb.1.5      S
+ 7  orf1a:del3675/3677          226006         243206  P.1 OR xbb.1.5  ORF1a
+
+                ref_aa        alt_aa  codon_num codon_end          type  \
+ 0                   R             K        203      None  substitution
+ 1                   D             G        614      None  substitution
+ 2                   P             L        314      None  substitution
+ 3                   H             Y        655      None  substitution
+ 4                   S             L         84      None  substitution
+ 5                   G             R        204      None  substitution
+ 6                   N             Y        501      None  substitution
+ 7  ORF1A:DEL3675/3677  DEL3675/3677       3675    3677.0      deletion
+
+    prevalence change_length_nt
+ 0    0.978528             None
+ 1    0.997188             None
+ 2    0.995970             None
+ 3    0.994075             None
+ 4    0.987295             None
+ 5    0.979010             None
+ 6    0.968948             None
+ 7    0.929278              9.0
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/lineage_prevalence.html b/lineage_prevalence.html new file mode 100644 index 0000000..3f6dfad --- /dev/null +++ b/lineage_prevalence.html @@ -0,0 +1,252 @@ + + + + + + + Lineage Prevalence Analysis — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Lineage Prevalence Analysis

+

The outbreak_data package has contains multiple endpoints that can collect information on SARS-CoV-2 lineages. Pulling data from a combination of endpoints will allow you to conduct your own analysis on the progression of SARS-CoV-2. On this page, you’ll find a few example workflows that demonstrate how to collect, manipulate, and visualize prevalence data in SARS-CoV-2 lineages.

+

Here is how we would go about collecting data to find all the XBB lineages prevalent in India within a 1-year timeframe:

+
# Perform authentication if you haven't already
+from outbreak_data import authenticate_user
+authenticate_user.authenticate_new_user()
+
+# Import outbreak_data package
+from outbreak_data import outbreak_data as od
+
+# Get the prevalence of all circulating XBB lineages in India
+data = od.prevalence_by_location("IND", startswith = 'xbb')
+# multiply prevalence values by 100% for scale
+data['prevalence_rolling'] = data['prevalence_rolling'].apply(lambda x: x*100)
+# Search for data based on date range
+data = data.sort_values(by="date")
+data = data.loc[data["date"].between("2020-09-12", "2022-03-31")]
+
+## Use the visual package of your choice to create an area graph using your data
+import altair as alt
+
+# Graph of results
+alt.Chart(data, title = "Lineage Prevalence in India").mark_area().encode(
+x='date:T',
+y=alt.Y('prevalence_rolling:Q'),
+color = 'lineage:N')
+
+
+
+
Output:
+
            date  total_count  lineage_count     lineage  prevalence  \
+ 3014 2022-09-12            0              0    xbb.1.16    0.000000
+ 3781 2022-09-12            0              0     xbb.2.3    0.000000
+ 2593 2022-09-12          152              2       xbb.1    0.013158
+ 3782 2022-09-13            0              0     xbb.2.3    0.000000
+ 3015 2022-09-13            0              0    xbb.1.16    0.000000
+ ...         ...          ...            ...         ...         ...
+ 4086 2023-03-31          196              2   xbb.2.3.2    0.010204
+ 3322 2023-03-31          196             29  xbb.1.16.1    0.147959
+ 2793 2023-03-31          196              1       xbb.1    0.005102
+ 3381 2023-03-31          196              7  xbb.1.16.2    0.035714
+ 3981 2023-03-31          196             15     xbb.2.3    0.076531
+
+      prevalence_rolling
+ 3014            0.000000
+ 3781            0.000000
+ 2593            0.003451
+ 3782            0.000000
+ 3015            0.000000
+ ...                  ...
+ 4086            0.031184
+ 3322            0.144578
+ 2793            0.014174
+ 3381            0.045358
+ 3981            0.084337
+[985 rows x 6 columns]
+
+
+
+_images/prev_visual.png +
+

Note

+

The Vega-Altair visualization package is used for demonstration purposes. However, any Python visual package can be used to create graphical representations of the data.

+
+

Finding the Most Prevalent Lineages

+

If we wanted to determine and plot the top four most prevalent lineages in India, we can make a few queries and use a few simple commands to create a table that shows us what these lineages are:

+
data=od.prevalence_by_location("IND")
+most_prev = data.groupby('lineage').apply(max) # Finds the lineages with the most hits
+most_prev = most_prev.mask(most_prev == '').dropna(how = 'any') # Drop any unknowns
+most_prev = most_prev.iloc[:4]
+print(most_prev)
+
+
+
+
Output
+
                  date  total_count  lineage_count    lineage  prevalence  \
+ lineage
+ ba.2       2023-04-20         5668           1445       ba.2    0.822785
+ ba.2.10.1  2023-04-19         5668             93  ba.2.10.1    0.285714
+ bq.1.1     2023-03-27          402              7     bq.1.1    0.428571
+ ch.1.1     2023-02-13          119              4     ch.1.1    0.400000
+
+            prevalence_rolling
+ lineage
+ ba.2                 0.677541
+ ba.2.10.1            0.095541
+ bq.1.1               0.156863
+ ch.1.1               0.066667
+
+
+
+

Next we’ll collect the prevalence data on each of the four lineages:

+
# Retrieve the official data on the prevalences of these lineages using `daily_prev()`
+d1 = od.daily_prev('ba.2', "IND")
+d2 = od.daily_prev('ba.2.10.1', "IND")
+d3 = od.daily_prev('bq.1.1', "IND")
+d4 = od.daily_prev( 'ch.1.1', "IND")
+
+# Formatting for creating the graph
+d1['lineage'] = 'ba.2'
+d2['lineage'] = 'ba.2.10.1'
+d3['lineage'] = 'bq.1.1'
+d4['lineage'] = 'ch.1.1'
+
+# Group together data from each lineage
+data = pd.concat([d1, d2, d3, d4])
+data = data.rename(columns = {'proportion': 'proportion (%)'})
+
+#Pick a date range to analyze
+data = data.sort_values(by="date")
+data = data.loc[data["date"].between("2022-09-12", "2023-03-31")]
+# Increase prevalence by 100%
+data['proportion'] = data['proportion'].apply(lambda x: x*100)
+
+#Graph using preferred visual package
+import altair as alt
+alt.Chart(data, title = "Top 4 Most Prevalent Lineages in India").mark_area().encode(
+x='date:T',
+y=alt.Y('proportion (%):Q'),
+color = 'lineage:N')
+
+
+_images/top4.png +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/location_details.html b/location_details.html new file mode 100644 index 0000000..13da6d8 --- /dev/null +++ b/location_details.html @@ -0,0 +1,150 @@ + + + + + + + location_details(location) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

location_details(location)

+
+
+outbreak_data.location_details(location, server='api.outbreak.info')
+

Get location details using location ID.

+
+
Arguments:
+
location:
+

A string. (Required).

+
+
return:
+

Some pandas dataframes.

+
+
+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/mutation_analysis.html b/mutation_analysis.html new file mode 100644 index 0000000..b3aa2e9 --- /dev/null +++ b/mutation_analysis.html @@ -0,0 +1,283 @@ + + + + + + + Viral Mutation Analysis — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

Viral Mutation Analysis

+

Lineage_Mutations Heatmap

+

A basic but important question: how do we define a lineage? What mutations consistently appear in most sequences within a lineage? We could start by plotting some of the characteristic mutations of XBB occurring in 80% of sequences. Even better, we can do this for mulitple related lineages and compare them using a heatmap:

+
# Perform authentication if you haven't already
+from outbreak_data import authenticate_user
+authenticate_user.authenticate_new_user()
+
+# Import outbreak_data package
+from outbreak_data import outbreak_data as od
+
+
+# Collecting 15 characteristic mutations and their prevalences for each variant
+
+lin0 = od.lineage_mutations("xbb", freq = 0.80)
+lin0["lineage"] = "xbb"
+lin0 = lin0.iloc[:15]
+
+lin1 = od.lineage_mutations("xbb.1", freq = 0.80)
+lin1["lineage"] = "xbb.1"
+lin1 = lin1.iloc[:15]
+
+lin2 = od.lineage_mutations("xbb.1.5", freq = 0.80)
+lin2["lineage"] = "xbb.1.5"
+lin2 = lin2.iloc[:15]
+
+lin3 = od.lineage_mutations("xbb.1.16", freq = 0.80)
+lin3["lineage"] = "xbb.1.16"
+lin3 = lin3.iloc[:15]
+
+lin4 = od.lineage_mutations("xbb.1.9", freq = 0.80)
+lin4["lineage"] = "xbb.1.9"
+lin4 = lin4.iloc[:15]
+
+lin5 = od.lineage_mutations("xbb.2.3", freq = 0.80)
+lin5["lineage"] = "xbb.2.3"
+lin5 = lin5.iloc[:15]
+
+# Link each of the findings together for plotting
+df = pd.concat([lin0, lin1, lin2, lin3, lin4, lin5])
+df["prevalence"] = df["prevalence"].apply(lambda x: x*100)
+df= df.rename(columns={'prevalence': 'prevalence %'})
+
+# Plot mutation heatmap
+import altair as alt
+
+alt.Chart(df).mark_rect().encode(
+    x = "mutation:N",
+    y = "lineage:N",
+    color = 'prevalence %:Q')
+
+
+
+
Output
+
         mutation  mutation_count  lineage_count  lineage   gene ref_aa alt_aa  \
+ 0      orf6:d61l            4198           4423      xbb   ORF6      D      L
+ 1         s:l24s            3919           4423      xbb      S      L      S
+ 2        n:r203k            4378           4423      xbb      N      R      K
+ 3        s:g339h            4054           4423      xbb      S      G      H
+ 4        s:v445p            3643           4423      xbb      S      V      P
+ ...           ...             ...            ...      ...    ...    ...    ...
+ 10  orf1a:p3395h            3263           3279  xbb.2.3  ORF1a      P      H
+ 11       s:n969k            3261           3279  xbb.2.3      S      N      K
+ 12  orf1a:g1307s            3257           3279  xbb.2.3  ORF1a      G      S
+ 13       s:d614g            3257           3279  xbb.2.3      S      D      G
+ 14       s:q954h            3257           3279  xbb.2.3      S      Q      H
+
+     codon_num codon_end          type  prevalence % change_length_nt
+ 0          61      None  substitution     94.912955             None
+ 1          24      None  substitution     88.605019             None
+ 2         203      None  substitution     98.982591             None
+ 3         339      None  substitution     91.657246             None
+ 4         445      None  substitution     82.364911             None
+ ...        ...       ...           ...           ...              ...
+ 10       3395      None  substitution     99.512046             None
+ 11        969      None  substitution     99.451052             None
+ 12       1307      None  substitution     99.329064             None
+ 13        614      None  substitution     99.329064             None
+ 14        954      None  substitution     99.329064             None
+
+
+
+

[90 rows x 12 columns]

+_images/mut_by_lin.png +

Comparing Lineages

+

To better understand the evolution of SARS-CoV-2, we may also want to know what mutations are shared between different viral lineages and how many shared mutations there are.

+

For this example we’ll look at three different lineages: B.1.1.7, P.1, and B.1.1.529. First, let’s get an idea of which mutations are shared between all three lineages:

+
lin1 = od.lineage_mutations("b.1.1.7")
+lin1["lineage"] = "b.1.1.7"
+
+lin2 = od.lineage_mutations("P.1")
+lin2["lineage"] = "P.1"
+
+lin3 = od.lineage_mutations("b.1.1.529")
+lin3["lineage"] = "b.1.1.529"
+
+#Finding intersections
+
+#Created an optional but convenient intersecting function
+def intersect(lst1, lst2):
+    return set(lst1).intersection(lst2)
+
+a = set(lin1['mutation'])
+b = set(lin2['mutation'])
+c = set(lin3['mutation'])
+
+m12 = intersect(a, b)
+m13 = intersect(a, c)
+m23 = intersect(b, c)
+m123 = intersect(m12, c)
+
+print('Set 1.2:', m12)
+print('Set 1.3:', m13)
+print('Set 2.3:' , m23)
+print('Set 1.2.3:', m123)
+
+
+
+
Output
+
 Set 1.2: {'orf1b:p314l', 'orf8:s84l', 'orf1a:del3675/3677', 'n:r203k', 's:d614g', 's:n501y', 'n:g204r'}
+ Set 1.3: {'s:p681h', 'orf1b:p314l', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'}
+ Set 2.3: {'orf1b:p314l', 's:h655y', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'}
+ Set 1.2.3: {'orf1b:p314l', 'orf8:s84l', 'n:r203k', 's:d614g', 'n:g204r'}
+
+
+
+

Finally, we can make a visual based on our findings and create a Venn diagram of our results:

+
# Import libraries for venn diagram visual
+from matplotlib_venn import venn3, venn3_circles
+from matplotlib import pyplot as plt
+
+# Using matplotlib_venn to make venn diagram with custom visuals
+ ## The venn diagram package used here automatically determines the number
+ ## of intersecting values and plots accordingly
+
+vd3 = venn3([a, b, c], set_labels = ('Alpha/B.1.1.7', 'Gamma/P.1', 'Omicron/B.1.1.529'), set_colors=('#c4e6ff', '#F4ACB7','#9D8189'),
+ alpha = 0.8)
+c = venn3_circles([a, b, c,], linestyle = '-.', linewidth=2, color='grey')
+for text in vd3.set_labels:
+ text.set_fontsize(16);
+for text in vd3.subset_labels:
+ text.set_fontsize(16)
+plt.title('Number of Overlapping Mutations in 3 Variants',fontname ='Helvetica',fontweight ='bold',fontsize = 18,
+ pad = 30,backgroundcolor ='#cbe7e3',color ='black', style ='normal');
+c[0].set_lw(7.0)
+c[0].set_ls(':')
+plt.show()
+
+
+_images/compare.png +

We can see that the graph matches the number of intersecting mutations that we previously saw, given that the venn diagram also takes into account unique values for each set.

+
+

Note

+

Please see the matplotlib venn diagram documentation and this article for more info on how to create these graphs.

+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/mutation_details.html b/mutation_details.html new file mode 100644 index 0000000..44b8122 --- /dev/null +++ b/mutation_details.html @@ -0,0 +1,172 @@ + + + + + + + mutation_details(mutations) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mutation_details(mutations)

+
+
+outbreak_data.mutation_details(mutations, server='api.outbreak.info')
+

Returns details of a mutation.

+
+
Arguments:
+
mutations:
+

(Required). Comma separated list of mutations.

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +

Example usage:

+
#Get info on mutation 'orf1b:p314l'
+df = outbreak_data.mutation_details('orf1b:p314l')
+print(df)
+
+
+
+
Output
+
             Key        Values
+ 0       mutation   ORF1b:P314L
+ 1      alt_codon           CTT
+ 2  is_synonymous         False
+ 3      codon_num           314
+ 4      ref_codon           CCT
+ 5           gene         ORF1b
+ 6            pos         14407
+ 7         alt_aa             L
+ 8         ref_aa             P
+ 9           type  substitution
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/mutations_by_lineage.html b/mutations_by_lineage.html new file mode 100644 index 0000000..5ca1faa --- /dev/null +++ b/mutations_by_lineage.html @@ -0,0 +1,205 @@ + + + + + + + mutations_by_lineage(mutation, location, pango_lin) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

mutations_by_lineage(mutation, location, pango_lin)

+
+
+outbreak_data.mutations_by_lineage(mutation=None, location=None, pango_lin=None, lineage_crumbs=False, datemin=None, datemax=None, freq=None, server='api.outbreak.info')
+

Returns the prevalence of a mutation or series of mutations across specified lineages by location

+
+
Arguments:
+
mutations:
+

(Optional). List or string of mutations separated by “,”.

+
+
location_id:
+

(Optional). A string; If not specified, return most recent date globally.

+
+
pangolin_lineage:
+

(Optional). If not specfied, returns all Pango lineages containing that mutation.

+
+
lineage_crumbs:
+

If true returns data for descendant lineages of pango_lin. Include the wildcard symbol ‘*’ in string to return info on all related lineages.

+
+
frequency:
+

(Optional) Minimimum frequency threshold for the prevalence of a mutation in a lineage.

+
+
datemin:
+

(Optional). A string representing the first cutoff date for returned date. Must be in YYYY-MM-DD format and be before ‘datemax’

+
+
datemax:
+

(Optional). A string representing the second cutoff date. Must be in YYY-MM-DD format and be after ‘datemin’

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +

Example usage:

+
#Get info on mutation 'orf1b:p314l'
+df = od.mutations_by_lineage('orf1b:p314l')
+print(df)
+
+
+
+
Output
+
         pangolin_lineage  lineage_count  mutation_count  proportion  \
+ 0                   ba.2        1227503         1222717    0.996101
+ 1                b.1.1.7        1154337         1147331    0.993931
+ 2                 ba.1.1        1044480         1039813    0.995532
+ 3                   ay.4         858839          854935    0.995454
+ 4                   ba.1         438947          437207    0.996036
+ ...                  ...            ...             ...         ...
+ 2851                fn.1              1               1    1.000000
+ 2852  miscba1ba2post5386              1               1    1.000000
+ 2853            xbb.1.23              1               1    1.000000
+ 2854            xbb.1.37              1               1    1.000000
+ 2855                 xbv              1               1    1.000000
+
+       proportion_ci_lower  proportion_ci_upper
+ 0                0.995990             0.996210
+ 1                0.993788             0.994071
+ 2                0.995402             0.995658
+ 3                0.995310             0.995595
+ 4                0.995847             0.996219
+ ...                   ...                  ...
+ 2851             0.146746             0.999614
+ 2852             0.146746             0.999614
+ 2853             0.146746             0.999614
+ 2854             0.146746             0.999614
+ 2855             0.146746             0.999614
+
+
+
+

[2856 rows x 6 columns]

+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/objects.inv b/objects.inv new file mode 100644 index 0000000..3eefc94 Binary files /dev/null and b/objects.inv differ diff --git a/outbreak_data_Functions.html b/outbreak_data_Functions.html new file mode 100644 index 0000000..1fb4ca4 --- /dev/null +++ b/outbreak_data_Functions.html @@ -0,0 +1,164 @@ + + + + + + + get_outbreak_data() — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

get_outbreak_data()

+
+

Note

+

This is a hidden function.

+
+
+
+outbreak_data.get_outbreak_data(endpoint, argstring, server='api.outbreak.info', auth=None, collect_all=False, curr_page=0)
+

Receives raw data using outbreak API.

+
+
Arguments:
+
endpoint:
+

directory in server the data is stored

+
+
argstring:
+

feature arguments to provide to API call

+
+
server:
+

Server to request from

+
+
auth:
+

Auth key (defaults to acceptable state)

+
+
collect_all:
+

if True, returns all data.

+
+
curr_page:
+

iterator state for paging

+
+
return:
+

A request object containing the raw data

+
+
+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/outbreak_data_functions.html b/outbreak_data_functions.html new file mode 100644 index 0000000..010945e --- /dev/null +++ b/outbreak_data_functions.html @@ -0,0 +1,173 @@ + + + + + + + get_outbreak_data() — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

get_outbreak_data()

+
+

Note

+

This is a hidden function.

+
+
+
+outbreak_data.get_outbreak_data(endpoint, argstring, server='api.outbreak.info', auth=None, collect_all=False, curr_page=0)
+

Receives raw data using outbreak API.

+
+
Arguments:
+
endpoint:
+

directory in server the data is stored

+
+
argstring:
+

feature arguments to provide to API call

+
+
server:
+

Server to request from

+
+
auth:
+

Auth key (defaults to acceptable state)

+
+
collect_all:
+

if True, returns all data.

+
+
curr_page:
+

iterator state for paging

+
+
return:
+

A request object containing the raw data

+
+
+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/prevalence_by_location.html b/prevalence_by_location.html new file mode 100644 index 0000000..1e9964f --- /dev/null +++ b/prevalence_by_location.html @@ -0,0 +1,240 @@ + + + + + + + prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None, lineage_crumbs=False) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None, lineage_crumbs=False)
    • +
  • + View page source +
    • +
+
+
+
+
+ +
+

prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None, lineage_crumbs=False)

+
+
+outbreak_data.prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None, server='api.outbreak.info')
+

Returns the daily prevalence of a PANGO lineage by location.

+
+
Arguments:
+
pango_lin:
+

(Required). List of lineages separated by ,

+
+
location_id:
+

(Optional). Default location: USA

+
+
mutations:
+

(Optional). List of mutations separated by AND

+
+
cumulative:
+

(Optional). If true returns the cumulative global prevalence since the first day of detection.

+
+
datemin:
+

(Optional). A string representing the first cutoff date for returned date. Must be in YYYY-MM-DD format and be before ‘datemax’

+
+
datemax:
+

(Optional). A string representing the second cutoff date. Must be in YYY-MM-DD format and be after ‘datemin’

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +

Example usage:

+
    +

  1. Get the daily prevalence of lineage ‘BA.2’ in India since first detection:

    +
    df1 = od.daily_prev('ba.2', "IND")
+print(df1)
+
    +
    +
    2. +
+
+
Output
+
             date  total_count  lineage_count  total_count_rolling  \
+ 0     2020-08-01           39              1            29.000000
+ 1     2020-08-02          100              0            41.285714
+ 2     2020-08-03           38              0            42.000000
+ 3     2020-08-04           20              0            42.285714
+ 4     2020-08-05           26              0            36.000000
+ ...          ...          ...            ...                  ...
+ 1017  2023-05-15            2              0             5.857143
+ 1018  2023-05-16            3              0             5.142857
+ 1019  2023-05-17            3              0             3.285714
+ 1020  2023-05-18            2              0             3.142857
+ 1021  2023-05-20            1              0             2.000000
+
+       lineage_count_rolling  proportion  proportion_ci_lower  \
+ 0                  0.142857    0.004926             0.000017
+ 1                  0.142857    0.003460             0.000012
+ 2                  0.142857    0.003401             0.000012
+ 3                  0.142857    0.003378             0.000012
+ 4                  0.142857    0.003968             0.000014
+ ...                     ...         ...                  ...
+ 1017               0.000000    0.000000             0.000078
+ 1018               0.000000    0.000000             0.000093
+ 1019               0.000000    0.000000             0.000151
+ 1020               0.000000    0.000000             0.000151
+ 1021               0.000000    0.000000             0.000217
+
+       proportion_ci_upper
+ 0                0.082286
+ 1                0.059076
+ 2                0.057719
+ 3                0.057719
+ 4                0.066944
+ ...                   ...
+ 1017             0.330389
+ 1018             0.379377
+ 1019             0.535583
+ 1020             0.535583
+ 1021             0.666822
+
+
+
+
    +

  1. Get a cumulative summary of information regarding ‘BA.2’ in India:

    +
    df2 = od.daily_prev('ba.2', "IND", cumulative = True)
+print(df2)
+
    +
    +
    2. +
+
+
Output
+
                        Values
+ first_detected     2020-08-01
+ global_prevalence    0.109641
+ last_detected      2023-04-26
+ lineage_count           25561
+ total_count            233134
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/search.html b/search.html new file mode 100644 index 0000000..697f159 --- /dev/null +++ b/search.html @@ -0,0 +1,145 @@ + + + + + + Search — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+
    +
    • +
  • Search
    • +
  • +
    • +
+
+
+
+
+ + + + +
+ +
+ +
+
+ +
+
+
+
+ + + + + + + + + \ No newline at end of file diff --git a/searchindex.js b/searchindex.js new file mode 100644 index 0000000..0e8a82c --- /dev/null +++ b/searchindex.js @@ -0,0 +1 @@ +Search.setIndex({"docnames": ["all_lineage_prevalences", "auth_setup", "cases_by_location", "collection_date", "cryptic_vars", "daily_lag", "epidem_analysis", "global_prevalence", "growth_rates", "index", "lineage_by_sub_admin", "lineage_mutations", "lineage_prevalence", "location_details", "mutation_analysis", "mutation_details", "mutations_by_lineage", "outbreak_data_functions", "prevalence_by_location", "seq_counts", "submission_date", "wildcard_lineage", "wildcard_location", "wildcard_mutations"], "filenames": ["all_lineage_prevalences.rst", "auth_setup.rst", "cases_by_location.rst", "collection_date.rst", "cryptic_vars.rst", "daily_lag.rst", "epidem_analysis.rst", "global_prevalence.rst", "growth_rates.rst", "index.rst", "lineage_by_sub_admin.rst", "lineage_mutations.rst", "lineage_prevalence.rst", "location_details.rst", "mutation_analysis.rst", "mutation_details.rst", "mutations_by_lineage.rst", "outbreak_data_functions.rst", "prevalence_by_location.rst", "seq_counts.rst", "submission_date.rst", "wildcard_lineage.rst", "wildcard_location.rst", "wildcard_mutations.rst"], "titles": ["all_lineage_prevalences(location, startswith)", "authenticate_new_user()", "cases_by_location(location)", "collection_date(pango_lin, mutations=None, location=None)", "Tracing Mutations Back to Lineage", "daily_lag(location=None)", "Working with epidemiological data", "global_prevalence(pango_lin, mutations, cumulative, lineage_crumbs=False)", "growth_rates(lineage, location)", "Welcome to the Python Outbreak.info package docs!", "lineage_by_sub_admin(pango_lin, mutations, location, ndays=0, detected)", "lineage_mutations(pango_lin, mutation, freq)", "Lineage Prevalence Analysis", "location_details(location)", "Viral Mutation Analysis", "mutation_details(mutations)", "mutations_by_lineage(mutation, 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7, "25": 7, "717": 7, "000027": 7, "558329e": 7, "000026": 7, "439232e": 7, "000025": [7, 10], "271630e": 7, "129377e": 7, "145063e": 7, "001271": 7, "374452e": 7, "888011e": 7, "354537e": 7, "944577e": 7, "949030e": 7, "000233": 7, "000211": 7, "000212": [7, 10], "022129": 7, "039548": 7, "094683": 7, "262217": 7, "718": 7, "growth": 8, "rate": 8, "score": 8, "given": [8, 14], "analyz": [9, 12], "pull": [9, 12], "reflect": 9, "web": 9, "interfac": 9, "recommend": 9, "via": 9, "pip": 9, "altern": 9, "directli": 9, "sourc": 9, "git": 9, "http": 9, "github": 9, "com": 9, "epidemiolog": 9, "log": 9, "gisaid": 9, "credenti": 9, "gener": 9, "an": [9, 10, 12, 14], "need": 9, "run": 9, "should": 9, "rest": 9, "compon": 9, "lin_list": 9, "351": 9, "617": 9, "occur": [9, 14], "lineage_mut": [9, 14], "freq": [9, 14, 16], "filter": 9, "codon": 9, "suppli": 9, "appropri": 9, "code": 9, "correspond": 9, "interest": 9, "id": [9, 10, 13], "lookup": 9, "kit": 9, "outbreak_tool": 9, "part": 9, "location_list": 9, "id_lookup": 9, "illinoi": 9, "south": 9, "africa": 9, "chile": 9, "il": 9, "zaf": 9, "chl": 9, "project": 9, "activ": 9, "develop": 9, "all_lineage_preval": 9, "startswith": [9, 12], "pango_lin": 9, "lineage_by_sub_admin": 9, "submission_d": 9, "mutation_detail": 9, "daily_lag": 9, "wildcard_lineag": 9, "wildcard_loc": 9, "wildcard_mut": 9, "location_detail": 9, "get_outbreak_data": 9, "growth_rat": 9, "deal": 9, "cryptic": 9, "logic": 10, "integ": 10, "calcul": 10, "cumu": 10, "limit": 10, "least": 10, "fra": 10, "fra_fr": 10, "31": [10, 12], "bretagn": 10, "bt": 10, "cors": 10, "ce": 10, "grand": 10, "est": 10, "ao": 10, "68": 10, "normandi": 10, "nd": 10, "occitani": 10, "lp": 10, "pai": 10, "de": 10, "loir": 10, "pl": 10, "cum_total_count": 10, "cum_lineage_count": 10, "406320": 10, "265376e": 10, "22070": 10, "000045": 10, "888926e": 10, "2007": 10, "446305e": 10, "43954": 10, "000023": 10, "454796e": 10, "19479": 10, "520808e": 10, "57933": 10, "475868e": 10, "24556": 10, "999632e": 10, "000044": 10, "001251": 10, "000106": 10, "000129": 10, "000043": 10, "000102": 10, "combin": 12, "conduct": 12, "your": 12, "own": 12, "progress": 12, "On": 12, "few": 12, "workflow": 12, "manipul": 12, "would": 12, "go": 12, "year": 12, "timefram": 12, "circul": 12, "multipli": 12, "scale": 12, "appli": [12, 14], "lambda": [12, 14], "base": [12, 14], "area": 12, "result": [12, 14], "mark_area": 12, "3014": 12, "3781": 12, "2593": 12, "152": 12, "013158": 12, "3782": 12, "3015": 12, "4086": 12, "196": 12, "010204": 12, "3322": 12, "147959": 12, "2793": 12, "005102": 12, "3381": 12, "035714": 12, "3981": 12, "076531": 12, "003451": 12, "031184": 12, "144578": 12, "014174": 12, "045358": 12, "084337": 12, "985": 12, "top": 12, "make": [12, 14], "simpl": 12, "command": 12, "tabl": 12, "show": [12, 14], "most_prev": 12, "groupbi": 12, "max": 12, "hit": 12, "mask": 12, "dropna": 12, "drop": 12, "unknown": 12, "iloc": [12, 14], "5668": 12, "1445": 12, "822785": 12, "bq": 12, "ch": 12, "119": 12, "400000": 12, "677541": 12, "095541": 12, "156863": 12, "066667": 12, "next": 12, "each": [12, 14], "offici": 12, "d1": 12, "d2": 12, "d3": 12, "d4": 12, "group": 12, "togeth": [12, 14], "pick": 12, "prefer": 12, "heatmap": 14, "basic": 14, "question": 14, "defin": 14, "appear": 14, "could": 14, "80": 14, "better": 14, "mulitpl": 14, "compar": 14, "lin0": 14, "lin4": 14, "lin5": 14, "link": 14, "mark_rect": 14, "orf6": 14, "d61l": 14, "4198": 14, "4423": 14, "l24": 14, "3919": 14, "4378": 14, "g339h": 14, "4054": 14, "v445p": 14, "3643": 14, "v": 14, "p3395h": 14, "3263": 14, "3279": 14, "n969k": 14, "3261": 14, "g1307": 14, "3257": 14, "q954h": 14, "94": 14, "912955": 14, "24": 14, "88": 14, "605019": 14, "98": 14, "982591": 14, "339": 14, "91": 14, "657246": 14, "445": 14, "82": 14, "364911": 14, "3395": 14, "99": 14, "512046": 14, "969": 14, "451052": 14, "1307": 14, "329064": 14, "954": 14, "understand": 14, "evolut": 14, "know": 14, "share": 14, "differ": 14, "529": 14, "idea": 14, "intersect": 14, "conveni": 14, "def": 14, "lst1": 14, "lst2": 14, "set": 14, "m12": 14, "m13": 14, "m23": 14, "m123": 14, "final": 14, "venn": 14, "diagram": 14, "librari": 14, "matplotlib_venn": 14, "venn3": 14, "venn3_circl": 14, "matplotlib": 14, "pyplot": 14, "plt": 14, "custom": 14, "automat": 14, "accordingli": 14, "vd3": 14, "set_label": 14, "alpha": 14, "gamma": 14, "set_color": 14, "c4e6ff": 14, "f4acb7": 14, "9d8189": 14, "linestyl": 14, "linewidth": 14, "grei": 14, "text": 14, "set_fonts": 14, "subset_label": 14, "fontnam": 14, "helvetica": 14, "fontweight": 14, "bold": 14, "fontsiz": 14, "pad": 14, "backgroundcolor": 14, "cbe7e3": 14, "black": 14, "style": 14, "normal": 14, "set_lw": 14, "set_l": 14, "match": [14, 21, 22, 23], "previous": 14, "saw": 14, "take": 14, "account": 14, "uniqu": 14, "pleas": 14, "document": 14, "articl": 14, "datemin": [9, 16], "datemax": [9, 16], "seri": 16, "across": 16, "specfi": 16, "symbol": 16, "minimimum": 16, "1227503": 16, "1222717": 16, "996101": 16, "1044480": 16, "1039813": 16, "995532": 16, "858839": 16, "854935": 16, "995454": 16, "438947": 16, "437207": 16, "996036": 16, "2851": 16, "fn": 16, "2852": 16, "miscba1ba2post5386": 16, "2853": 16, "23": 16, "2854": 16, "37": 16, "2855": 16, "xbv": 16, "995990": 16, "996210": 16, "993788": 16, "994071": 16, "995402": 16, "995658": 16, "995310": 16, "995595": 16, "995847": 16, "996219": 16, "146746": 16, "999614": 16, "2856": 16, "end": [21, 22, 23], "unit": 22, "e484": 23, "sequence_count": 9, "sub_admin": 9}, "objects": {"authenticate_user": [[1, 0, 1, "", "authenticate_new_user"]], "outbreak_data": [[0, 0, 1, "", "all_lineage_prevalences"], [2, 0, 1, "", "cases_by_location"], [3, 0, 1, "", "collection_date"], [5, 0, 1, "", "daily_lag"], [17, 0, 1, "", "get_outbreak_data"], [7, 0, 1, "", "global_prevalence"], [8, 0, 1, "", "growth_rates"], [10, 0, 1, "", "lineage_by_sub_admin"], [11, 0, 1, "", "lineage_mutations"], [13, 0, 1, "", "location_details"], [15, 0, 1, "", "mutation_details"], [16, 0, 1, "", "mutations_by_lineage"], [18, 0, 1, "", "prevalence_by_location"], [19, 0, 1, "", "sequence_counts"], [20, 0, 1, "", "submission_date"], [21, 0, 1, "", "wildcard_lineage"], [22, 0, 1, "", "wildcard_location"], [23, 0, 1, "", "wildcard_mutations"]]}, "objtypes": {"0": "py:function"}, "objnames": {"0": ["py", "function", "Python function"]}, "titleterms": {"cases_by_loc": 2, "locat": [0, 2, 3, 5, 8, 10, 13, 16, 18, 19, 20], "lineage_mut": 11, "pango_lin": [3, 7, 10, 11, 16, 18, 20], "mutat": [3, 4, 7, 10, 11, 14, 15, 16, 18, 20], "freq": 11, "get_outbreak_data": 17, "prevalence_by_loc": 18, "none": [3, 5, 18, 20], "datemin": 18, "datemax": 18, "cumul": [7, 18, 19], "sequence_count": 19, "sub_admin": 19, "all_lineage_preval": 0, "startswith": 0, "authenticate_new_us": 1, "collection_d": 3, "trace": 4, "back": 4, "lineag": [4, 8, 12], "daily_lag": 5, "work": 6, "epidemiolog": 6, "data": [6, 9], "global_preval": 7, "growth_rat": 8, "welcom": 9, "python": 9, "outbreak": 9, "info": 9, "packag": 9, "doc": 9, "instal": 9, "get": 9, "start": 9, "core": 9, "tool": 9, "exampl": 9, "analys": 9, "lineage_by_sub_admin": 10, "ndai": 10, "0": 10, "detect": 10, "preval": 12, "analysi": [12, 14], "location_detail": 13, "viral": 14, "mutation_detail": 15, "mutations_by_lineag": 16, "submission_d": 20, "wildcard_lineag": 21, "name": [21, 22, 23], "wildcard_loc": 22, "wildcard_mut": 23, "lineage_crumb": [7, 18], "fals": [7, 18]}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 60}, "alltitles": {"all_lineage_prevalences(location, startswith)": [[0, "all-lineage-prevalences-location-startswith"]], "authenticate_new_user()": [[1, "authenticate-new-user"]], "collection_date(pango_lin, mutations=None, location=None)": [[3, "collection-date-pango-lin-mutations-none-location-none"]], "Tracing Mutations Back to Lineage": [[4, "tracing-mutations-back-to-lineage"]], "daily_lag(location=None)": [[5, "daily-lag-location-none"]], "Working with epidemiological data": [[6, "working-with-epidemiological-data"]], "growth_rates(lineage, location)": [[8, "growth-rates-lineage-location"]], "lineage_by_sub_admin(pango_lin, mutations, location, ndays=0, detected)": [[10, "lineage-by-sub-admin-pango-lin-mutations-location-ndays-0-detected"]], "Lineage Prevalence Analysis": [[12, "lineage-prevalence-analysis"]], "location_details(location)": [[13, "location-details-location"]], "Viral Mutation Analysis": [[14, "viral-mutation-analysis"]], "mutation_details(mutations)": [[15, "mutation-details-mutations"]], "mutations_by_lineage(mutation, location, pango_lin)": [[16, "mutations-by-lineage-mutation-location-pango-lin"]], "submission_date(pango_lin, mutations=None, location)": [[20, "submission-date-pango-lin-mutations-none-location"]], "wildcard_lineage(name)": [[21, "wildcard-lineage-name"]], "wildcard_location(name)": [[22, "wildcard-location-name"]], "wildcard_mutations(name)": [[23, "wildcard-mutations-name"]], "cases_by_location(location)": [[2, "cases-by-location-location"]], "lineage_mutations(pango_lin, mutation, freq)": [[11, "lineage-mutations-pango-lin-mutation-freq"]], "sequence_counts(location, cumulative, sub_admin)": [[19, "sequence-counts-location-cumulative-sub-admin"]], "Welcome to the Python Outbreak.info package docs!": [[9, "welcome-to-the-python-outbreak-info-package-docs"]], "Installation": [[9, "installation"]], "Getting Started": [[9, "getting-started"]], "Core Outbreak Data Tools": [[9, "core-outbreak-data-tools"]], "Example analyses:": [[9, "example-analyses"]], "get_outbreak_data()": [[17, "get-outbreak-data"]], "global_prevalence(pango_lin, mutations, cumulative, lineage_crumbs=False)": [[7, "global-prevalence-pango-lin-mutations-cumulative-lineage-crumbs-false"]], "prevalence_by_location(pango_lin, location, mutations=None, datemin=None, datemax=None, cumulative=None, lineage_crumbs=False)": [[18, "prevalence-by-location-pango-lin-location-mutations-none-datemin-none-datemax-none-cumulative-none-lineage-crumbs-false"]]}, "indexentries": {"prevalence_by_location() (in module outbreak_data)": [[18, "outbreak_data.prevalence_by_location"]]}}) \ No newline at end of file diff --git a/seq_counts.html b/seq_counts.html new file mode 100644 index 0000000..3bc981d --- /dev/null +++ b/seq_counts.html @@ -0,0 +1,199 @@ + + + + + + + sequence_counts(location, cumulative, sub_admin) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

sequence_counts(location, cumulative, sub_admin)

+
+
+outbreak_data.sequence_counts(location=None, cumulative=None, sub_admin=None, server='api.outbreak.info')
+

Returns number of sequences per day by location

+
+
Arguments:
+
location:
+

(Optional). If not specified, the global total counts are returned.

+
+
cumulative:
+

(Optional). If true returns the cumulative number of sequences till date.

+
+
subadmin:
+

(Optional). If true and cumulative=true, returns the cumulative number of sequences for the immedaite lower admin level.

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +

Example usage:

+
    +

  1. Get number of daily sequence counts in the US:

    +
    df = od.sequence_counts('USA')
+print(df)
+
    +
    +
    2. +
+
+
Output
+
            Key        Values
+ 0       mutation   ORF1b:P314L
+ 1      alt_codon           CTT
+ 2  is_synonymous         False
+ 3      codon_num           314
+ 4      ref_codon           CCT
+ 5           gene         ORF1b
+ 6            pos         14407
+ 7         alt_aa             L
+ 8         ref_aa             P
+ 9           type  substitution
+
+
+
+
    +

  1. Get total number of sequence counts

    +
    +

    df = od.sequence_counts(‘USA’, cumulative=True) +print(df)

    +
    +
    2. +
+
+
Output
+
               Values
+ total_count  4617418
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/submission_date.html b/submission_date.html new file mode 100644 index 0000000..b5e4143 --- /dev/null +++ b/submission_date.html @@ -0,0 +1,169 @@ + + + + + + + submission_date(pango_lin, mutations=None, location) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

submission_date(pango_lin, mutations=None, location)

+
+
+outbreak_data.submission_date(pango_lin, mutations=None, location=None, server='api.outbreak.info')
+

Returns the most recent submission date by location

+
+
Arguments:
+
pango_lin:
+

A string. (Required).

+
+
mutations:
+

(Optional). A string or list of strings. Comma separated list of mutations.

+
+
location:
+

(Optional). If not specified, return most recent date globally.

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +

Example usage:

+
df = outbreak_data.submission_date('xbb.1', location='USA')
+print(df)
+
+
+
+
Output
+
                 Values
+ date        2023-06-16
+ date_count           5
+
+
+
+
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/wildcard_lineage.html b/wildcard_lineage.html new file mode 100644 index 0000000..0926395 --- /dev/null +++ b/wildcard_lineage.html @@ -0,0 +1,150 @@ + + + + + + + wildcard_lineage(name) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

wildcard_lineage(name)

+
+
+outbreak_data.wildcard_lineage(name, server='api.outbreak.info')
+

Match lineage name using wildcards.

+
+
Arguments:
+
name:
+

(Required). A string. Must use * at end of string. Supports wildcards. (Example: b.1*, ba.2*)

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/wildcard_location.html b/wildcard_location.html new file mode 100644 index 0000000..28a689d --- /dev/null +++ b/wildcard_location.html @@ -0,0 +1,150 @@ + + + + + + + wildcard_location(name) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

wildcard_location(name)

+
+
+outbreak_data.wildcard_location(name, server='api.outbreak.info')
+

Match location name using wildcards.

+
+
Arguments:
+
name:
+

(Required). A string. Must use * at end of string. Supports wildcards. (Example: united*)

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file diff --git a/wildcard_mutations.html b/wildcard_mutations.html new file mode 100644 index 0000000..e347ea7 --- /dev/null +++ b/wildcard_mutations.html @@ -0,0 +1,150 @@ + + + + + + + wildcard_mutations(name) — Python Outbreak.info API 0.1 documentation + + + + + + + + + + + + + + + + + + + +
+ + +
+ +
+
+
+ +
+
+
+
+ +
+

wildcard_mutations(name)

+
+
+outbreak_data.wildcard_mutations(name, server='api.outbreak.info')
+

Match mutations using wildcards.

+
+
Arguments:
+
name:
+

(Required) A string. Must use * at end of string. Supports wildcards. (Example: s:e484*)

+
+
return:
+

A pandas dataframe.

+
+
+
+
+
+ +
+ + +
+
+ +
+
+
+
+ + + + \ No newline at end of file