prep for update

Author: smasongarrison

NAMESPACE

@@ -39,6 +39,7 @@ export(readWikifamilytree)
 export(readgedcom)
 export(recodeSex)
 export(related_coef)
+export(repairIDs)
 export(repairSex)
 export(resample)
 export(simulatePedigree)

NEWS.md

@@ -1,5 +1,7 @@
 # BGmisc 1.4.1
+## In Progress
 * replaced print with message in all functions
+* Exposed several internal functions to the user
 
 # BGmisc 1.4.0
 * revived checkParents function to check for handling phantom parents and missing parents

R/checkIDs.R

@@ -89,6 +89,7 @@ checkIDs <- function(ped, verbose = FALSE, repair = FALSE) {
 #' This function repairs missing IDs in a pedigree.
 #' @inheritParams checkIDs
 #' @return A corrected pedigree
+#' @export
 repairIDs <- function(ped, verbose = FALSE) {
   checkIDs(ped = ped, verbose = verbose, repair = TRUE)
 }

R/cleanPedigree.R

@@ -9,7 +9,6 @@
 #' @param verbose A logical indicating whether to print progress messages.
 #' @return A dataframe with standardized column names.
 #'
-#' @keywords internal
 standardizeColnames <- function(df, verbose = FALSE) {
   # Internal mapping of standardized names to possible variants
   mapping <- list(
@@ -25,7 +24,7 @@ standardizeColnames <- function(df, verbose = FALSE) {
     "sex" = "^(?:sex|gender|female|m(?:a(?:le|n)|en)|wom[ae]n)"
   )
   if (verbose) {
-    print("Standardizing column names...")
+    message("Standardizing column names...")
   }
   lowered_colnames <- tolower(colnames(df))
   for (standard_name in names(mapping)) {

R/helpPedigree.R

@@ -63,6 +63,7 @@ determineSex <- function(idGen, sexR, code_male = "M", code_female = "F") {
 #' @param df_Ngen The dataframe for the current generation, including columns for individual IDs and spouse IDs.
 #' @return The input dataframe augmented with a 'coupleId' column, where each mated pair has a unique identifier.
 #' @export
+#'
 assignCoupleIDs <- function(df_Ngen) {
   df_Ngen$coupleId <- NA_character_ # Initialize the coupleId column with NAs
   usedCoupleIds <- character() # Initialize an empty character vector to track used IDs