From 55849972c5569448052ebd96b9ba84381717cca4 Mon Sep 17 00:00:00 2001 From: Robert William Schlegel Date: Tue, 5 Dec 2023 11:01:58 +0100 Subject: [PATCH] Re-built site for new minor version --- DESCRIPTION | 4 ++-- docs/404.html | 2 +- docs/CITATIONS.html | 2 +- docs/CODE_OF_CONDUCT.html | 2 +- docs/CONTRIBUTING.html | 2 +- docs/LICENSE-text.html | 2 +- docs/LICENSE.html | 2 +- docs/articles/Download_SST_v2.html | 4 ++-- docs/articles/MHW_metric_trends.html | 4 ++-- docs/articles/MHW_to_nc.html | 4 ++-- docs/articles/OISST_preparation.html | 4 ++-- docs/articles/complex_clims.html | 4 ++-- .../articles/detection_and_visualisation.html | 4 ++-- docs/articles/event_categories.html | 4 ++-- docs/articles/exceedance.html | 4 ++-- docs/articles/gridded_event_detection.html | 4 ++-- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 5 +++-- docs/news/index.html | 6 +++++- docs/pkgdown.yml | 2 +- docs/reference/Algiers.html | 2 +- docs/reference/block_average.html | 2 +- docs/reference/category.html | 2 +- docs/reference/clim_calc.html | 2 +- docs/reference/clim_spread.html | 2 +- docs/reference/detect_event.html | 21 +++++++++++-------- docs/reference/detect_event3.html | 2 +- docs/reference/event_line.html | 2 +- docs/reference/exceedance.html | 2 +- docs/reference/geom_flame.html | 2 +- docs/reference/geom_lolli.html | 2 +- docs/reference/heatwaveR-package.html | 2 +- docs/reference/index.html | 2 +- docs/reference/lolli_plot.html | 2 +- docs/reference/make_whole_fast.html | 2 +- docs/reference/na_interp.html | 2 +- docs/reference/proto_event.html | 2 +- docs/reference/proto_event3.html | 2 +- docs/reference/smooth_percentile.html | 2 +- docs/reference/sst_Med.html | 2 +- docs/reference/sst_NW_Atl.html | 2 +- docs/reference/sst_WA.html | 2 +- docs/reference/ts2clm.html | 2 +- docs/reference/ts2clm3.html | 11 ++-------- 45 files changed, 73 insertions(+), 72 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1749bf12..675e3e85 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: heatwaveR -Version: 0.5.2.9005 -Date: 2023-11-11 +Version: 0.5.2.9006 +Date: 2023-12-05 Title: Detect Heatwaves and Cold-Spells Description: The different methods for defining, detecting, and categorising the extreme events known as heatwaves or cold-spells, as first proposed in Hobday et al. (2016) diff --git a/docs/404.html b/docs/404.html index 14aa63ba..4174f2d6 100644 --- a/docs/404.html +++ b/docs/404.html @@ -47,7 +47,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/CITATIONS.html b/docs/CITATIONS.html index 4f44e87c..ba51b517 100644 --- a/docs/CITATIONS.html +++ b/docs/CITATIONS.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html index da5ecbc2..b58a1c66 100644 --- a/docs/CODE_OF_CONDUCT.html +++ b/docs/CODE_OF_CONDUCT.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html index 0307d9f4..4f953cf1 100644 --- a/docs/CONTRIBUTING.html +++ b/docs/CONTRIBUTING.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index ff9d76f3..f30327fa 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 4c43ca1f..26679301 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/articles/Download_SST_v2.html b/docs/articles/Download_SST_v2.html index d1d2c4a9..8a0fa29e 100644 --- a/docs/articles/Download_SST_v2.html +++ b/docs/articles/Download_SST_v2.html @@ -48,7 +48,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -140,7 +140,7 @@

Download, Prepare, and Analyse NOAA OISST Data: Alternative Methods

AJ Smit

-

2023-11-11

+

2023-12-05

Source: vignettes/Download_SST_v2.Rmd diff --git a/docs/articles/MHW_metric_trends.html b/docs/articles/MHW_metric_trends.html index 0a63c873..2015dbe3 100644 --- a/docs/articles/MHW_metric_trends.html +++ b/docs/articles/MHW_metric_trends.html @@ -48,7 +48,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -141,7 +141,7 @@

Trend and Breakpoint analyses in MHW

Francois Thoral

-

2023-11-11

+

2023-12-05

Source: vignettes/MHW_metric_trends.Rmd diff --git a/docs/articles/MHW_to_nc.html b/docs/articles/MHW_to_nc.html index 7a248a6c..8fa07b64 100644 --- a/docs/articles/MHW_to_nc.html +++ b/docs/articles/MHW_to_nc.html @@ -48,7 +48,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -140,7 +140,7 @@

Saving MHW Results to NetCDF

Robert W Schlegel

-

2023-11-11

+

2023-12-05

Source: vignettes/MHW_to_nc.Rmd diff --git a/docs/articles/OISST_preparation.html b/docs/articles/OISST_preparation.html index ba4ef579..2bdf030b 100644 --- a/docs/articles/OISST_preparation.html +++ b/docs/articles/OISST_preparation.html @@ -48,7 +48,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -140,7 +140,7 @@

Downloading and Preparing NOAA OISST Data

Robert W Schlegel and AJ Smit

-

2023-11-11

+

2023-12-05

Source: vignettes/OISST_preparation.Rmd diff --git a/docs/articles/complex_clims.html b/docs/articles/complex_clims.html index fb843dfd..ba8a4326 100644 --- a/docs/articles/complex_clims.html +++ b/docs/articles/complex_clims.html @@ -48,7 +48,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -140,7 +140,7 @@

Alternative Thresholds

Robert W Schlegel

-

2023-11-11

+

2023-12-05

Source: vignettes/complex_clims.Rmd diff --git a/docs/articles/detection_and_visualisation.html b/docs/articles/detection_and_visualisation.html index b4d4b3d9..4178fa25 100644 --- a/docs/articles/detection_and_visualisation.html +++ b/docs/articles/detection_and_visualisation.html @@ -48,7 +48,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -140,7 +140,7 @@

Basic Detection and Visualisation of Events

AJ Smit and Robert W Schlegel

-

2023-11-11

+

2023-12-05

Source: vignettes/detection_and_visualisation.Rmd diff --git a/docs/articles/event_categories.html b/docs/articles/event_categories.html index f8e58fe2..312ddde2 100644 --- a/docs/articles/event_categories.html +++ b/docs/articles/event_categories.html @@ -48,7 +48,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -141,7 +141,7 @@

Calculating and Visualising Event

Robert W Schlegel

-

2023-11-11

+

2023-12-05

Source: vignettes/event_categories.Rmd diff --git a/docs/articles/exceedance.html b/docs/articles/exceedance.html index 1c36019f..c39466c9 100644 --- a/docs/articles/exceedance.html +++ b/docs/articles/exceedance.html @@ -48,7 +48,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -140,7 +140,7 @@

Calculating and Visualising Exceedances

Robert W Schlegel

-

2023-11-11

+

2023-12-05

Source: vignettes/exceedance.Rmd diff --git a/docs/articles/gridded_event_detection.html b/docs/articles/gridded_event_detection.html index 396b0d93..48841050 100644 --- a/docs/articles/gridded_event_detection.html +++ b/docs/articles/gridded_event_detection.html @@ -48,7 +48,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -140,7 +140,7 @@

Detecting Events in Gridded Data

Robert W Schlegel and AJ Smit

-

2023-11-11

+

2023-12-05

Source: vignettes/gridded_event_detection.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 50d5edb8..e4407288 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/authors.html b/docs/authors.html index b45c55df..eac09fe2 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/index.html b/docs/index.html index 4cf40997..9e172397 100644 --- a/docs/index.html +++ b/docs/index.html @@ -51,7 +51,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -144,7 +144,8 @@

CRAN_Status_Badge R-CMD-check Codecov test coverage JOSS DOI Downloads

The heatwaveR package is a project-wide update to the RmarineHeatWaves package, which is itself a translation of the original Python code written by Eric C. J. Oliver. The heatwaveR package also uses the same naming conventions for objects, columns, and arguments as the Python code.

The heatwaveR R package contains the original functions from the RmarineHeatWaves package that calculate and display marine heatwaves (MHWs) according to the definition of Hobday et al. (2016) as well as calculating and visualising marine cold-spells (MCSs) as first introduced in Schlegel et al. (2017a). It also contains the functionality to calculate the categories of MHWs as outlined in Hobday et al. (2018).

-

This package does what RmarineHeatWaves does, but faster. The entire package has been deconstructed and modularised, and we are continuing to implement slow portions of the code in C++. This has alleviated the bottlenecks that slowed down the climatology creation portions of the code as well as generally creating an overall increase in the speed of the calculations. Currently the R code runs about as fast as the original python functions, at least in as far as applying it to single time series of temperatures. Readers familiar with both languages will know about the ongoing debate around the relative speed of the two languages. In our experience, R can be as fast as python, provided that attention is paid to finding ways to reduce the computational inefficiencies that stem from i) the liberal use of complex and inefficient non-atomic data structures, such as data frames; ii) the reliance on non-vectorised calculations such as loops; and iii) lazy (but convenient) coding that comes from drawing too heavily on the tidyverse suite of packages. We will continue to ensure that heatwaveR becomes more-and-more efficient so that it can be applied to large gridded data products with ease. To that end, the extension package heatwave3 has been developed. This helps the user to apply the code from heatwaveR directly onto their NetCDF and other 3D gridded data files.

+

This package does what RmarineHeatWaves does, but faster. The entire package has been deconstructed and modularised, and we are continuing to implement slow portions of the code in C++. This has alleviated the bottlenecks that slowed down the climatology creation portions of the code as well as generally creating an overall increase in the speed of the calculations. Currently the R code runs about as fast as the original python functions, at least in as far as applying it to single time series of temperatures.

+

Readers familiar with both languages will know about the ongoing debate around the relative speed of the two languages. In our experience, R can be as fast as python, provided that attention is paid to finding ways to reduce the computational inefficiencies that stem from i) the liberal use of complex and inefficient non-atomic data structures, such as data frames; ii) the reliance on non-vectorised calculations such as loops; and iii) lazy (but convenient) coding that comes from drawing too heavily on the tidyverse suite of packages. We will continue to ensure that heatwaveR becomes more-and-more efficient so that it can be applied to large gridded data products with ease. To that end, the extension package heatwave3 has been developed. This helps the user to apply the code from heatwaveR directly onto their NetCDF and other 3D gridded data files.

heatwaveR was also developed and released in order to better accommodate the inclusion of the definitions of atmospheric heatwaves in addition to MHWs. Additionally, heatwaveR also provides the first implementation of a definition for a ‘compound heatwave’. There are currently multiple different definitions for this type of event and each of which has arguments provided for it within the ts2clm() and detect_event() functions.

This package may be installed from CRAN by typing the following command into the console:

install.packages("heatwaveR")

diff --git a/docs/news/index.html b/docs/news/index.html index 7164f7ea..5f1fa058 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -105,6 +105,10 @@

Changelog

Source: NEWS.md +
+

heatwaveR 0.5.2.9006 (2023-12-05)

+
  • Removed cpp function seqDates() from package
    • +

heatwaveR 0.5.2.9005 (2023-11-11)

  • Removed category functionality from detect_event3() to keep it more streamlined
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index bf43c237..b5b26d46 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -11,7 +11,7 @@ articles: event_categories: event_categories.html exceedance: exceedance.html gridded_event_detection: gridded_event_detection.html -last_built: 2023-11-11T06:32Z +last_built: 2023-12-05T09:59Z urls: reference: https://robwschlegel.github.io/heatwaveR/index.html/reference article: https://robwschlegel.github.io/heatwaveR/index.html/articles diff --git a/docs/reference/Algiers.html b/docs/reference/Algiers.html index 7f7ed412..be1529a4 100644 --- a/docs/reference/Algiers.html +++ b/docs/reference/Algiers.html @@ -25,7 +25,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006
diff --git a/docs/reference/block_average.html b/docs/reference/block_average.html index ec659d3a..cbaca49f 100644 --- a/docs/reference/block_average.html +++ b/docs/reference/block_average.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/category.html b/docs/reference/category.html index 23121ffb..8b265173 100644 --- a/docs/reference/category.html +++ b/docs/reference/category.html @@ -24,7 +24,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/clim_calc.html b/docs/reference/clim_calc.html index 8ef3602b..31dba2ba 100644 --- a/docs/reference/clim_calc.html +++ b/docs/reference/clim_calc.html @@ -24,7 +24,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/clim_spread.html b/docs/reference/clim_spread.html index a02bd917..a367976f 100644 --- a/docs/reference/clim_spread.html +++ b/docs/reference/clim_spread.html @@ -25,7 +25,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/detect_event.html b/docs/reference/detect_event.html index cb9b68df..5f7d8be8 100644 --- a/docs/reference/detect_event.html +++ b/docs/reference/detect_event.html @@ -27,7 +27,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -231,15 +231,18 @@

Arguments

protoEvents
-

Boolean specifying whether the original time series will be -returned with only the columns indicating whether or not the threshold criterion +

The default, protoEvents = FALSE, will return the full +output comprised of a list of two data frames, one with the climatology +and the other with the event metrics. See Value below. +If protoEvents = TRUE, the output will contain the original time series +together with columns indicating if the threshold criterion (threshCriterion) and duration criterion (durationCriterion) -have been exceeded, a column showing if a heatwave is present (i.e. both -threshCriterion and durationCriterion TRUE), and a -sequential number uniquely identifying the detected event(s). Therefore any heatwave -metrics will not be reported. The default is FALSE. Note also that if -protoEvents = TRUE it will ignore whatever the user provides to the categories -argument and anything else passed to ....

+have been exceeded, a column showing if a heatwave is present +(i.e. both threshCriterion and durationCriterion +TRUE), and a sequential number uniquely identifying the detected event(s); +heatwave metrics will not be reported in the event dataframe. Note also that +if protoEvents = TRUE it will ignore whatever the user provides to the +categories argument and anything else passed to ....

categories
diff --git a/docs/reference/detect_event3.html b/docs/reference/detect_event3.html index cb6f1892..209b58be 100644 --- a/docs/reference/detect_event3.html +++ b/docs/reference/detect_event3.html @@ -28,7 +28,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/event_line.html b/docs/reference/event_line.html index b3900e64..75d44087 100644 --- a/docs/reference/event_line.html +++ b/docs/reference/event_line.html @@ -24,7 +24,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/exceedance.html b/docs/reference/exceedance.html index f31c3dad..326c75ce 100644 --- a/docs/reference/exceedance.html +++ b/docs/reference/exceedance.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/geom_flame.html b/docs/reference/geom_flame.html index d3a79fa9..ccf0ec80 100644 --- a/docs/reference/geom_flame.html +++ b/docs/reference/geom_flame.html @@ -32,7 +32,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/geom_lolli.html b/docs/reference/geom_lolli.html index 68149960..887426a9 100644 --- a/docs/reference/geom_lolli.html +++ b/docs/reference/geom_lolli.html @@ -30,7 +30,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/heatwaveR-package.html b/docs/reference/heatwaveR-package.html index 5862fcb4..28ebbfd8 100644 --- a/docs/reference/heatwaveR-package.html +++ b/docs/reference/heatwaveR-package.html @@ -24,7 +24,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/index.html b/docs/reference/index.html index 1e8847f6..871d2033 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/lolli_plot.html b/docs/reference/lolli_plot.html index 22ec2771..dc58e75e 100644 --- a/docs/reference/lolli_plot.html +++ b/docs/reference/lolli_plot.html @@ -23,7 +23,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/make_whole_fast.html b/docs/reference/make_whole_fast.html index 7eb3e0fc..dbe74c27 100644 --- a/docs/reference/make_whole_fast.html +++ b/docs/reference/make_whole_fast.html @@ -24,7 +24,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/na_interp.html b/docs/reference/na_interp.html index a1aa8b72..df9b0e50 100644 --- a/docs/reference/na_interp.html +++ b/docs/reference/na_interp.html @@ -25,7 +25,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/proto_event.html b/docs/reference/proto_event.html index 3e91d300..8d62660b 100644 --- a/docs/reference/proto_event.html +++ b/docs/reference/proto_event.html @@ -24,7 +24,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/proto_event3.html b/docs/reference/proto_event3.html index a233c41c..42e07f3b 100644 --- a/docs/reference/proto_event3.html +++ b/docs/reference/proto_event3.html @@ -26,7 +26,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/smooth_percentile.html b/docs/reference/smooth_percentile.html index aba8a2aa..e1044c41 100644 --- a/docs/reference/smooth_percentile.html +++ b/docs/reference/smooth_percentile.html @@ -24,7 +24,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/sst_Med.html b/docs/reference/sst_Med.html index 1eb0e2fd..c5e2c828 100644 --- a/docs/reference/sst_Med.html +++ b/docs/reference/sst_Med.html @@ -24,7 +24,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/sst_NW_Atl.html b/docs/reference/sst_NW_Atl.html index a3ff9741..85c84d4d 100644 --- a/docs/reference/sst_NW_Atl.html +++ b/docs/reference/sst_NW_Atl.html @@ -24,7 +24,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/sst_WA.html b/docs/reference/sst_WA.html index 6c5b0a93..3bc13881 100644 --- a/docs/reference/sst_WA.html +++ b/docs/reference/sst_WA.html @@ -24,7 +24,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/ts2clm.html b/docs/reference/ts2clm.html index 8aca88c2..444a15e7 100644 --- a/docs/reference/ts2clm.html +++ b/docs/reference/ts2clm.html @@ -25,7 +25,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 diff --git a/docs/reference/ts2clm3.html b/docs/reference/ts2clm3.html index 14f1615a..7d617eb7 100644 --- a/docs/reference/ts2clm3.html +++ b/docs/reference/ts2clm3.html @@ -26,7 +26,7 @@ heatwaveR - 0.5.2.9005 + 0.5.2.9006 @@ -129,8 +129,7 @@

Make a climatology from a daily time series.

smoothPercentileWidth = 31, clmOnly = FALSE, var = FALSE, - roundClm = 4, - cppDate = FALSE + roundClm = 4 ) @@ -225,12 +224,6 @@

Arguments

prevent rounding set roundClm = FALSE. This argument may only be given numeric values or FALSE.

- -
cppDate
-

Boolean (default = FALSE) to indicate if the pre-compiled -C++ function seqDates should be used to fill any potential gaps in the given -time series.

-

Value