Add {epireview} SARS pathogen to core columns and coercion

R/coercion.R

@@ -258,12 +258,12 @@ is_epiparameter_df <- function(x) {
 
   pathogen <- .unique(x$pathogen, var_name = "pathogen")
   # get disease from pathogen lookup
-  disease <- switch(
-    pathogen,
+  disease <- switch(pathogen,
     "Marburg virus" = "Marburg Virus Disease",
     "Lassa mammarenavirus" = "Lassa fever",
     "Ebola virus" = "Ebola Virus Disease",
-    stop("Pathogen in epireview not recognised", call. = FALSE)
+    "SARS-CoV" = "Severe Acute Respiratory Syndrome (SARS)",
+    stop("Pathogen in {epireview} not recognised", call. = FALSE)
   )
   epi_name <- .unique(x$parameter_type, var_name = "parameter types")
   prob_dist <- .unique(x$distribution_type, var_name = "distribution types")

R/data.R

@@ -1,11 +1,9 @@
 #' A vector of `character` strings with the core column names of the
 #' epidemiological parameter data exported by the \pkg{epireview} R package.
 #'
-#' A subset of data from the World Health Organization Global Tuberculosis
-#' Report ...
-#'
 #' @format ## `epireview_core_cols`
-#' A `character` vector with 56 elements
+#' A `character` vector with `r length(epiparameter::epireview_core_cols)`
+#' elements.
 #'
 #' The data is taken as the intersection of the column names of each of the
 #' disease parameter tables in the \pkg{epireview} R package.

data-raw/epireview_core_cols.R

@@ -6,20 +6,23 @@ if (requireNamespace("epireview", quietly = TRUE)) {
   epireview_marburg <- epireview::load_epidata("marburg")
   epireview_ebola <- epireview::load_epidata("ebola")
   epireview_lassa <- epireview::load_epidata("lassa")
+  epireview_sars <- epireview::load_epidata("sars")
 
-  intersect_marburg_ebola <- intersect(
+  epireview_core_cols <- intersect(
     colnames(epireview_marburg$params),
     colnames(epireview_ebola$params)
   )
   epireview_core_cols <- intersect(
-    intersect_marburg_ebola,
+    epireview_core_cols,
     colnames(epireview_lassa$params)
   )
+  epireview_core_cols <- intersect(
+    epireview_core_cols,
+    colnames(epireview_sars$params)
+  )
   usethis::use_data(
     epireview_core_cols,
     overwrite = TRUE,
     version = 3
   )
 }
-
-