rename

Author: smasongarrison

R/checkIDs.R

@@ -41,7 +41,7 @@ checkIDs <- function(ped, verbose = FALSE, repair = FALSE) {
     cat("Validation Results:\n")
     message(validation_results)
   }
-  if (repair) {
+  if (repair == TRUE) {
     if (verbose == TRUE) {
       cat("Attempting to repair:\n")
       cat("Step 1: Attempting to repair non-unique IDs...\n")

R/insertEven.R R/helpInsertEven.RR/insertEven.R renamed to R/helpInsertEven.R

@@ -9,7 +9,6 @@
 #' The function takes two vectors, m and n, and inserts the elements of m evenly into n.
 #' If the length of m is greater than the length of n, the vectors are swapped, and the insertion proceeds.
 #' The resulting vector is a combination of m and n, with the elements of m evenly distributed within n.
-#' @export
 #' @seealso \code{\link{SimPed}} for the main function that uses this supporting function.
 
 insertEven <- function(m, n, verbose = FALSE) {

R/cleanPedigree.R R/helpNames.RR/cleanPedigree.R renamed to R/helpNames.R

@@ -41,6 +41,53 @@ standardizeColnames <- function(df, verbose = FALSE) {
 
   return(df)
 }
+#' Restore Original Column Names in a Pedigree Dataframe
+#'
+#' This function restores the original column names of a pedigree dataframe
+#' based on user-specified names. It is useful for reverting standardized column
+#' names back to their original names after processing.
+#' @param ped A pedigree dataframe with standardized column names.
+#' @param famID The original name for the family ID column. Default is "fam
+#' ID".
+#' @param personID The original name for the person ID column. Default is "ID".
+#' @param momID The original name for the mother ID column. Default is "momID".
+#' @param dadID The original name for the father ID column. Default is "dadID".
+#' @param gen The original name for the generation column. Default is "gen".
+#' @param patID The original name for the paternal ID column. Default is "patID".
+#' @param matID The original name for the maternal ID column. Default is "matID".
+#' @param spID The original name for the spouse ID column. Default is "spID".
+#' @param twinID The original name for the twin ID column. Default is "twinID".
+#' @param zygosity The original name for the zygosity column. Default is "zygosity".
+#' @param sex The original name for the sex column. Default is "sex".
+#' @return A pedigree dataframe with restored original column names.
+restorePedColnames <- function(ped,
+                               famID = "famID",
+                               personID = "ID",
+                               momID = "momID",
+                               dadID = "dadID",
+                               gen = "gen",
+                               patID = "patID",
+                               matID = "matID",
+                               spID = "spID",
+                               twinID = "twinID",
+                               zygosity = "zygosity",
+                               sex = "sex"
+) {
+
+  names(ped)[names(ped) == "ID"] <- personID
+  names(ped)[names(ped) == "momID"] <- momID
+  names(ped)[names(ped) == "dadID"] <- dadID
+  names(ped)[names(ped) == "famID"] <- famID
+  names(ped)[names(ped) == "gen"] <- gen
+  names(ped)[names(ped) == "patID"] <- patID
+  names(ped)[names(ped) == "matID"] <- matID
+  names(ped)[names(ped) == "spID"] <- spID
+  names(ped)[names(ped) == "twinID"] <- twinID
+  names(ped)[names(ped) == "zygosity"] <- zygosity
+  names(ped)[names(ped) == "sex"] <- sex
+  ped
+}
+
 
 
 # Repair Pedigree