Dev main

R/checkIDs.R

@@ -57,9 +57,11 @@ checkIDs <- function(ped, verbose = FALSE, repair = FALSE) {
     if (length(validation_results$non_unique_ids) > 0) {
       # loop through each non-unique ID
 
-      processed <- dropIdenticalDuplicateIDs(ped = repaired_ped,
+      processed <- dropIdenticalDuplicateIDs(
+        ped = repaired_ped,
         ids = validation_results$non_unique_ids,
-        changes = changes)
+        changes = changes
+      )
       repaired_ped <- processed$ped
       changes <- processed$changes
     }

R/checkParents.R

@@ -59,9 +59,6 @@ checkParentIDs <- function(ped, verbose = FALSE, repair = FALSE,
   validation_results$single_parents <- (length(missing_fathers) + length(missing_mothers)) > 0
 
 
-
-
-
   if (verbose && validation_results$single_parents) cat("Missing single parents found.\n")
   if (verbose && !validation_results$single_parents) cat("No missing single parents found.\n")
 
@@ -269,12 +266,12 @@ checkParentIDs <- function(ped, verbose = FALSE, repair = FALSE,
   }
 
   # restore orginal names that the user orginally provided
-  ped <-  restorePedColnames(ped,
+  ped <- restorePedColnames(ped,
     famID = famID,
     personID = personID,
     momID = momID,
-    dadID = dadID)
-
+    dadID = dadID
+  )
 }
 #' Repair Parent IDs
 #'

R/helpChecks.R

@@ -7,8 +7,7 @@
 #' @param ped A data frame representing the pedigree.
 #' @param ids A vector of IDs to check for duplicates in the pedigree.
 #' @param changes An optional list to log changes made during the process.
-dropIdenticalDuplicateIDs <- function(ped, ids, changes = NULL
-) {
+dropIdenticalDuplicateIDs <- function(ped, ids, changes = NULL) {
   if (!is.data.frame(ped)) {
     stop("ped must be a data frame")
   }