Cran reinstate msfdictrenamer

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: epidict
 Title: Epidemiology Data Dictionaries and Random Data Generators
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: c(
     person("Alexander", "Spina", , "aspina@appliedepi.org", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8425-1867")),
@@ -40,11 +40,12 @@ Suggests:
     knitr,
     matchmaker,
     rmarkdown,
+    sitrep, 
     testthat (>= 2.1.0),
     withr
 VignetteBuilder: 
     knitr
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NAMESPACE

@@ -3,6 +3,7 @@
 export(dict_rename_helper)
 export(gen_data)
 export(msf_dict)
+export(msf_dict_rename_helper)
 export(read_dict)
 importFrom(clipr,write_clip)
 importFrom(dplyr,bind_rows)

NEWS.md

@@ -1,3 +1,6 @@
+# epidict 0.2.0
+* Reinstate msf_dict_rename_helper() with sitrep in DESCRIPTION suggests 
+
 # epidict 0.1.0
 * First CRAN release 
 * Separated out functions for reading dictionaries 

R/msf_dict_rename_helper.R

@@ -1,66 +1,66 @@
-#' #' Helper for aligning your data to MSF standardised dictionaries and analysis templates.
-#' #'
-#' #' @param dictionary Specify which MSF dictionary you would like to use.
-#' #' See [msf_dict()] for options.
-#' #'
-#' #' @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
-#' #'
-#' #' @importFrom readxl read_excel
-#' #'
-#' #' @export
+#' Helper for aligning your data to MSF standardised dictionaries and analysis templates.
 #'
-#' msf_dict_rename_helper <- function(dictionary,
-#'                                    copy_to_clipboard = TRUE) {
+#' @param dictionary Specify which MSF dictionary you would like to use.
+#' See [msf_dict()] for options.
 #'
-#'   # just add dict as "empty" if not defined (for checking errors)
-#'   if (missing("dictionary")) {
-#'     dictionary <- "empty"
-#'     }
+#' @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.
 #'
-#'   # define dictionary types
-#'   dict <- get_dictionary(dictionary, org = "MSF")
-#'   disease <- unlist(dict, use.names = FALSE)
-#'   is_survey <- length(dict$survey) == 1
-#'   format <- ifelse(is_survey | grepl("_intersectional", disease),
-#'                   "ODK", "DHIS2")
+#' @return A dplyr command used to rename columns in your data frame according
+#' to the dictionary
 #'
-#'   # get dictionary
-#'   dat_dict <- msf_dict(dictionary = disease, compact = TRUE)
-#'
-#'   # define the dictionary columns for variable names and variable type
-#'   varnames <- ifelse(format == "ODK", "name", "data_element_shortname")
-#'   varnames_type <- ifelse(format == "ODK", "type", "data_element_valuetype")
-#'
-#'   # remove long and short from vaccination (only one template with 2 dicts)
-#'   if (disease == "vaccination_short" | disease == "vaccination_long") {
-#'     disease  <- "vaccination"
-#'   }
-#'
-#'   # only call sitrep if it's installed
-#'   if (!requireNamespace("sitrep", quietly = TRUE)) {
-#'     stop(
-#'       "The 'sitrep' package is required for this function but is not installed.\n",
-#'       "Please install it from GitHub: R4EPI/sitrep"
-#'     )
-#'   }
-#'
-#'   # get the outbreak Rmd to check if the variable is optional or required
-#'   outbreak_file <- sitrep::available_sitrep_templates(recursive = TRUE, pattern = ".Rmd", full.names = TRUE)
-#'   outbreak_file <- grep(tolower(disease), outbreak_file, value = TRUE)[[1]]
-#'
-#'   # call the dict_rename_helper function
-#'   dict_rename_helper(
-#'     dictionary = dat_dict,
-#'     varnames = varnames,
-#'     varnames_type = varnames_type,
-#'     rmd = outbreak_file,
-#'     copy_to_clipboard = copy_to_clipboard
-#'   )
-#'
-#' }
+#' @importFrom readxl read_excel
 #'
+#' @export
+
+msf_dict_rename_helper <- function(dictionary,
+                                   copy_to_clipboard = TRUE) {
+
+  # just add dict as "empty" if not defined (for checking errors)
+  if (missing("dictionary")) {
+    dictionary <- "empty"
+    }
+
+  # define dictionary types
+  dict <- get_dictionary(dictionary, org = "MSF")
+  disease <- unlist(dict, use.names = FALSE)
+  is_survey <- length(dict$survey) == 1
+  format <- ifelse(is_survey | grepl("_intersectional", disease),
+                  "ODK", "DHIS2")
+
+  # get dictionary
+  dat_dict <- msf_dict(dictionary = disease, compact = TRUE)
+
+  # define the dictionary columns for variable names and variable type
+  varnames <- ifelse(format == "ODK", "name", "data_element_shortname")
+  varnames_type <- ifelse(format == "ODK", "type", "data_element_valuetype")
+
+  # remove long and short from vaccination (only one template with 2 dicts)
+  if (disease == "vaccination_short" | disease == "vaccination_long") {
+    disease  <- "vaccination"
+  }
+
+  # only call sitrep if it's installed
+  if (!requireNamespace("sitrep", quietly = TRUE)) {
+    stop(
+      "The 'sitrep' package is required for this function but is not installed.\n",
+      "Please install it using install.packages('sitrep)"
+    )
+  }
+
+  # get the outbreak Rmd to check if the variable is optional or required
+  outbreak_file <- sitrep::available_sitrep_templates(recursive = TRUE, pattern = ".Rmd", full.names = TRUE)
+  outbreak_file <- grep(tolower(disease), outbreak_file, value = TRUE)[[1]]
+
+  # call the dict_rename_helper function
+  dict_rename_helper(
+    dictionary = dat_dict,
+    varnames = varnames,
+    varnames_type = varnames_type,
+    rmd = outbreak_file,
+    copy_to_clipboard = copy_to_clipboard
+  )
+
+}
+

cran-comments.md

@@ -7,17 +7,8 @@
 
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
+0 errors | 0 warnings | 0 note
 
-* This is a new submission to CRAN.*
-
-All URLs and metadata issues noted in the previous submission have been corrected:
-- Updated Title field to title case.
-- possible misspelled words in DESCRIPTION are correct as is. 
-- Updated all URLs to canonical HTTPS versions with trailing slashes.
-- Updated lifecycle badge link to https://lifecycle.r-lib.org/articles/stages.html#maturing.
-- Spelled out acronyms.
-- description spacing fixed and link added to describe methods 
-- value descriptions added to functions 
+- new function added for a minor release