Dev datasets (#40)

* Remove year_init and year_end from the default dataset serodata * Remove year_init and year_end from the default dataset chagas2012 * Remove year_init and year_end from the dataset chik2015 * Remove year_init and year_end from the dataset veev2012 * doc: remove year_init and year_end from documentation
epiverse-trace · Mar 30, 2023 · 7a1baa2 · 7a1baa2
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diff --git a/R/modelling.R b/R/modelling.R
@@ -11,8 +11,6 @@
 #' \code{counts} \tab Number of positive samples for each age group\cr \tab \cr
 #' \code{age_min} \tab age_min \cr \tab \cr
 #' \code{age_max} \tab age_max \cr \tab \cr
-#' \code{year_init} \tab year_init \cr \tab \cr
-#' \code{year_end} \tab year_end \cr \tab \cr
 #' \code{tsur} \tab Year in which the survey took place \cr \tab \cr
 #' \code{country} \tab The country where the survey took place \cr \tab \cr
 #' \code{test} \tab The type of test taken \cr \tab \cr

diff --git a/R/seroprevalence_data.R b/R/seroprevalence_data.R
@@ -9,8 +9,6 @@
 #' \code{counts} \tab Number of positive samples for each age group\cr \tab \cr
 #' \code{age_min} \tab age_min \cr \tab \cr
 #' \code{age_max} \tab age_max \cr \tab \cr
-#' \code{year_init} \tab year_init \cr \tab \cr
-#' \code{year_end} \tab year_end \cr \tab \cr
 #' \code{tsur} \tab Year in which the survey took place \cr \tab \cr
 #' \code{country} \tab The country where the survey took place \cr \tab \cr
 #' \code{test} \tab The type of test taken \cr \tab \cr
@@ -74,8 +72,6 @@ prepare_serodata <- function(serodata = serodata,
 #' \code{counts} \tab Number of positive samples for each age group\cr \tab \cr
 #' \code{age_min} \tab age_min \cr \tab \cr
 #' \code{age_max} \tab age_max \cr \tab \cr
-#' \code{year_init} \tab year_init \cr \tab \cr
-#' \code{year_end} \tab year_end \cr \tab \cr
 #' \code{tsur} \tab Year in which the survey took place \cr \tab \cr
 #' \code{country} \tab The country where the survey took place \cr \tab \cr
 #' \code{test} \tab The type of test taken \cr \tab \cr

diff --git a/R/visualization.R b/R/visualization.R
@@ -8,8 +8,6 @@
 #' \code{counts} \tab Number of positive samples for each age group\cr \tab \cr
 #' \code{age_min} \tab age_min \cr \tab \cr
 #' \code{age_max} \tab age_max \cr \tab \cr
-#' \code{year_init} \tab year_init \cr \tab \cr
-#' \code{year_end} \tab year_end \cr \tab \cr
 #' \code{tsur} \tab Year in which the survey took place \cr \tab \cr
 #' \code{country} \tab The country where the survey took place \cr \tab \cr
 #' \code{test} \tab The type of test taken \cr \tab \cr

diff --git a/README.md b/README.md
@@ -46,12 +46,12 @@ The package provides an example dataset of the observed serosurvey data,
 # Load example serodata data included with the package
 data(serodata)
 head(serodata, 5)
-#>       survey total counts age_min age_max year_init year_end tsur country  test
-#> 1 COL-035-93    34      0       1       1      2012     2012 2012     COL ELISA
-#> 2 COL-035-93    25      0       2       2      2012     2012 2012     COL ELISA
-#> 3 COL-035-93    35      1       3       3      2012     2012 2012     COL ELISA
-#> 4 COL-035-93    29      0       4       4      2012     2012 2012     COL ELISA
-#> 5 COL-035-93    36      0       5       5      2012     2012 2012     COL ELISA
+#>       survey total counts age_min age_max tsur country  test
+#> 1 COL-035-93    34      0       1       1 2012     COL ELISA
+#> 2 COL-035-93    25      0       2       2 2012     COL ELISA
+#> 3 COL-035-93    35      1       3       3 2012     COL ELISA
+#> 4 COL-035-93    29      0       4       4 2012     COL ELISA
+#> 5 COL-035-93    36      0       5       5 2012     COL ELISA
 #>           antibody
 #> 1 IgG anti-T.cruzi
 #> 2 IgG anti-T.cruzi

diff --git a/data/chagas2012.RDS b/data/chagas2012.RDS
diff --git a/data/chagas2012.RData b/data/chagas2012.RData
diff --git a/data/chik2015.RDS b/data/chik2015.RDS
diff --git a/data/chik2015.RData b/data/chik2015.RData
diff --git a/data/serodata.RDS b/data/serodata.RDS
diff --git a/data/serodata.RData b/data/serodata.RData
diff --git a/data/veev2012.RDS b/data/veev2012.RDS
diff --git a/data/veev2012.RData b/data/veev2012.RData
diff --git a/man/get_exposure_matrix.Rd b/man/get_exposure_matrix.Rd
diff --git a/man/get_prev_expanded.Rd b/man/get_prev_expanded.Rd
diff --git a/man/plot_seroprev.Rd b/man/plot_seroprev.Rd
diff --git a/man/prepare_bin_data.Rd b/man/prepare_bin_data.Rd
diff --git a/man/prepare_serodata.Rd b/man/prepare_serodata.Rd
diff --git a/man/run_seromodel.Rd b/man/run_seromodel.Rd