add in survey to rename helper for #15

R/msf_dict_rename_helper.R

@@ -2,38 +2,68 @@
 #'
 #' @export
 #' @param disease Specify which disease you would like to use.
-#'   Currently supports "Cholera", "Measles" and "Meningitis", "AJS".
+#'   Currently supports "Cholera", "Measles", "Meningitis", "AJS",
+#'   "Mortality", "Nutrition", "Vaccination_short" and "Vaccination_long".
 #'
 #' @param varnames Specify name of column that contains varnames. Currently
-#'   default set to "Item".  (this can probably be deleted once dictionaries
-#'   standardise) If `dictionary` is "Mortality", `varnames` needs to be "column_name"`.
-#' 
+#'   default set to "data_element_shortname".
+#'   If `dictionary` is a survey ("Mortality", "Nutrition", "Vaccination_short"
+#'   or "Vaccination_long") `varnames` needs to be "name"`.
+#'
 #' @param copy_to_clipboard if `TRUE` (default), the rename template will be
 #'   copied to the user's clipboard with [clipr::write_clip()]. If `FALSE`, the
 #'   rename template will be printed to the user's console.
 #'
 #' @return a dplyr command used to rename columns in your data frame according
 #' to the dictionary
 msf_dict_rename_helper <- function(disease, varnames = "data_element_shortname", copy_to_clipboard = TRUE) {
-  # get msf disease specific data dictionary
-  dat_dict <- msf_dict(disease = disease, compact = TRUE)
+
+  # make disease name lower case
+  disease <- tolower(disease)
+
+  # get msf disease specific outbreak data dictionary
+  if (disease == "cholera" | disease ==  "measles" |
+      disease == "meningitis" | disease == "ajs") {
+
+    dat_dict <- msf_dict(disease = disease, compact = TRUE)
+
+    # define the name of the column in the dictionary which has variable class
+    var_type_col <- "data_element_valuetype"
+  }
+
+  # get msf disease specific survey data dictionary
+  if (disease == "mortality" | disease == "nutrition" |
+      disease == "vaccination_short" | disease == "vaccination_long") {
+
+    dat_dict <- msf_dict_survey(disease, compact = TRUE)
+
+    # define the name of the column in the dictionary which has variable class
+    var_type_col <- "type"
+  }
+
+  # change vaccinations to be one
+  if (disease == "vaccination_short" | disease == "vaccination_long") {
+
+    disease  <- "vaccination"
+  }
+
   # get the outbreak Rmd to check if the variable is optional or required
   outbreak_file <- available_sitrep_templates(recursive = TRUE, pattern = ".Rmd", full.names = TRUE)
-  outbreak_file <- grep(tolower(disease), outbreak_file, value = TRUE)[[1]]
+  outbreak_file <- grep(disease, outbreak_file, value = TRUE)[[1]]
   outbreak_file <- readLines(outbreak_file)
 
-  dat_dict[["var_required"]] <- vapply(dat_dict[[varnames]], 
-    FUN = function(i, o) if (any(grepl(paste0("^[^#]*", i), o))) "REQUIRED" else "optional", 
-    FUN.VALUE = character(1), 
+  dat_dict[["var_required"]] <- vapply(dat_dict[[varnames]],
+    FUN = function(i, o) if (any(grepl(paste0("^[^#]*", i), o))) "REQUIRED" else "optional",
+    FUN.VALUE = character(1),
     o = outbreak_file
   )
-  dat_dict <- dat_dict[order(dat_dict[["var_required"]] != "REQUIRED", 
+  dat_dict <- dat_dict[order(dat_dict[["var_required"]] != "REQUIRED",
                              dat_dict[[varnames]]), ]
   msg <- "## Add the appropriate column names after the equals signs\n\n"
   msg <- paste0(msg, "linelist_cleaned <- rename(linelist_cleaned,\n")
   the_renames <- sprintf("  %s =   , # %s (%s)",
     format(dat_dict[[varnames]]),
-    format(dat_dict[["data_element_valuetype"]]),
+    format(dat_dict[[var_type_col]]),
     dat_dict[["var_required"]]
   )
   the_renames[length(the_renames)] <- gsub(",", " ", the_renames[length(the_renames)])