From a7a20965eb6e535afa4b7cf920368b3a28186232 Mon Sep 17 00:00:00 2001
From: Mason Garrison <garrissm@wfu.edu>
Date: Wed, 28 Jan 2026 08:37:54 -0500
Subject: [PATCH 1/6] rename

---
 R/checkIDs.R                         |  2 +-
 R/{insertEven.R => helpInsertEven.R} |  2 --
 R/{cleanPedigree.R => helpNames.R}   | 47 ++++++++++++++++++++++++++++
 3 files changed, 48 insertions(+), 3 deletions(-)
 rename R/{insertEven.R => helpInsertEven.R} (98%)
 rename R/{cleanPedigree.R => helpNames.R} (73%)

diff --git a/R/checkIDs.R b/R/checkIDs.R
index 3b518388..b3f8adae 100644
--- a/R/checkIDs.R
+++ b/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")
diff --git a/R/insertEven.R b/R/helpInsertEven.R
similarity index 98%
rename from R/insertEven.R
rename to R/helpInsertEven.R
index 3c35b915..284e8445 100644
--- a/R/insertEven.R
+++ b/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) {
@@ -55,5 +54,4 @@ insertEven <- function(m, n, verbose = FALSE) {
 }
 
 #' @rdname insertEven
-#' @export
 evenInsert <- insertEven
diff --git a/R/cleanPedigree.R b/R/helpNames.R
similarity index 73%
rename from R/cleanPedigree.R
rename to R/helpNames.R
index 1605bc60..46406f0d 100644
--- a/R/cleanPedigree.R
+++ b/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

From 5bc027ba9a838ffe85830673b5a5b666255a3fd8 Mon Sep 17 00:00:00 2001
From: Mason Garrison <garrissm@wfu.edu>
Date: Wed, 28 Jan 2026 09:19:24 -0500
Subject: [PATCH 2/6] Add helper functions for pedigree checks and refactor

Introduces helper functions addIfAny and dropIdenticalDuplicateIDs to streamline pedigree validation and repair logic. Refactors checkIDs and checkParents to use these helpers, improving code clarity and modularity. Enhances restorePedColnames to be more robust and adds documentation for new helpers.
---
 NAMESPACE                        |  2 --
 NEWS.md                          |  3 ++
 R/checkIDs.R                     | 19 ++++-------
 R/checkParents.R                 | 25 ++++++++-------
 R/helpChecks.R                   | 47 +++++++++++++++++++++++++++
 R/helpNames.R                    | 53 +++++++++++++++++++++++-------
 man/addIfAny.Rd                  | 22 +++++++++++++
 man/dropIdenticalDuplicateIDs.Rd | 19 +++++++++++
 man/insertEven.Rd                |  2 +-
 man/restorePedColnames.Rd        | 55 ++++++++++++++++++++++++++++++++
 man/standardizeColnames.Rd       |  2 +-
 11 files changed, 208 insertions(+), 41 deletions(-)
 create mode 100644 R/helpChecks.R
 create mode 100644 man/addIfAny.Rd
 create mode 100644 man/dropIdenticalDuplicateIDs.Rd
 create mode 100644 man/restorePedColnames.Rd

diff --git a/NAMESPACE b/NAMESPACE
index babeb73d..2b4a4878 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -17,12 +17,10 @@ export(computeParentAdjacency)
 export(createGenDataFrame)
 export(determineSex)
 export(dropLink)
-export(evenInsert)
 export(fitComponentModel)
 export(getWikiTreeSummary)
 export(identifyComponentModel)
 export(inferRelatedness)
-export(insertEven)
 export(makeInbreeding)
 export(makeTwins)
 export(ped2add)
diff --git a/NEWS.md b/NEWS.md
index ed537985..2a3c973f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,7 @@
 # BGmisc NEWS
+# Development version: 1.6.0.9000
+
+* Add helper functions for checkParents etc
 
 # BGmisc 1.6
 * Optimize  simulatePedigree and helpers for speed and memory usage
diff --git a/R/checkIDs.R b/R/checkIDs.R
index b3f8adae..05f104c1 100644
--- a/R/checkIDs.R
+++ b/R/checkIDs.R
@@ -56,19 +56,12 @@ checkIDs <- function(ped, verbose = FALSE, repair = FALSE) {
     # if there are non-unique IDs
     if (length(validation_results$non_unique_ids) > 0) {
       # loop through each non-unique ID
-      for (id in validation_results$non_unique_ids) {
-        rows_with_id <- repaired_ped[repaired_ped$ID == id, ]
-        # If all rows with the same ID are truly identical, keep only the first occurrence
-        if (nrow(unique(rows_with_id)) == 1) {
-          # Mark as removed in the changes list
-          changes[[paste0("ID", id)]] <- "Removed duplicates"
-          # Keep only the first row, remove the rest
-          repaired_ped <- repaired_ped[-which(repaired_ped$ID == id)[-1], ] # Remove all but the first occurrence
-        } else {
-          # Mark as kept in the changes list
-          changes[[paste0("ID", id)]] <- "Kept duplicates"
-        }
-      }
+
+      processed <- dropIdenticalDuplicateIDs(ped = repaired_ped,
+        ids = validation_results$non_unique_ids,
+        changes = changes)
+      repaired_ped <- processed$ped
+      changes <- processed$changes
     }
     if (verbose == TRUE) {
       cat("Step 2: No repair for parents who are their children at this time\n")
diff --git a/R/checkParents.R b/R/checkParents.R
index 3a2216d6..2abe3e24 100644
--- a/R/checkParents.R
+++ b/R/checkParents.R
@@ -52,14 +52,14 @@ checkParentIDs <- function(ped, verbose = FALSE, repair = FALSE,
   missing_mothers <- ped$ID[which(!is.na(ped$dadID) & is.na(ped$momID))]
 
   # Update the validation_results list
-  if (length(missing_fathers) > 0) {
-    validation_results$missing_fathers <- missing_fathers
-  }
-  if (length(missing_mothers) > 0) {
-    validation_results$missing_mothers <- missing_mothers
-  }
 
-  validation_results$single_parents <- length(validation_results) > 0
+  validation_results <- addIfAny(validation_results, "missing_fathers", missing_fathers)
+  validation_results <- addIfAny(validation_results, "missing_mothers", missing_mothers)
+
+  validation_results$single_parents <- (length(missing_fathers) + length(missing_mothers)) > 0
+
+
+
 
 
   if (verbose && validation_results$single_parents) cat("Missing single parents found.\n")
@@ -269,11 +269,12 @@ checkParentIDs <- function(ped, verbose = FALSE, repair = FALSE,
   }
 
   # restore orginal names that the user orginally provided
-  names(ped)[names(ped) == "ID"] <- personID
-  names(ped)[names(ped) == "momID"] <- momID
-  names(ped)[names(ped) == "dadID"] <- dadID
-  names(ped)[names(ped) == "famID"] <- famID
-  return(ped)
+  ped <-  restorePedColnames(ped,
+    famID = famID,
+    personID = personID,
+    momID = momID,
+    dadID = dadID)
+
 }
 #' Repair Parent IDs
 #'
diff --git a/R/helpChecks.R b/R/helpChecks.R
new file mode 100644
index 00000000..eb233bb3
--- /dev/null
+++ b/R/helpChecks.R
@@ -0,0 +1,47 @@
+#' Drop Identical Duplicate IDs from Pedigree Data Frame
+#'
+#' #' This function identifies and removes duplicate entries in a pedigree data frame
+#' based on a list of specified IDs. If multiple rows share the same ID and are
+#' identical, only one instance is retained. The function returns the modified pedigree
+#' data frame along with a log of changes made.
+#' @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
+) {
+  if (!is.data.frame(ped)) {
+    stop("ped must be a data frame")
+  }
+  if (is.null(changes)) {
+    changes <- list()
+  } else if (!is.list(changes)) {
+    stop("changes must be a list or NULL")
+  }
+
+  out <- ped
+
+  if (!is.null(ids) && length(ids) > 0) {
+    for (id in ids) {
+      rows_with_id <- out[out$ID == id, , drop = FALSE]
+      if (nrow(unique(rows_with_id)) == 1) {
+        changes[[paste0("ID", id)]] <- "Removed duplicates"
+        out <- out[-which(out$ID == id)[-1], , drop = FALSE]
+      } else {
+        changes[[paste0("ID", id)]] <- "Kept duplicates"
+      }
+    }
+  }
+
+  list(ped = out, changes = changes)
+}
+
+#' Helper function to conditionally add elements to a list
+#' @param validation A list to which elements may be added.
+#' @param name A character string representing the name of the element to add.
+#' @param value The value to add to the list if it is not NULL or empty
+#' @return The updated list with the new element added if applicable.
+#' @keywords internal
+addIfAny <- function(validation, name, value) {
+  if (!is.null(value) && length(value) > 0) validation[[name]] <- value
+  validation
+}
diff --git a/R/helpNames.R b/R/helpNames.R
index 46406f0d..9ef3c674 100644
--- a/R/helpNames.R
+++ b/R/helpNames.R
@@ -71,20 +71,49 @@ restorePedColnames <- function(ped,
                                spID = "spID",
                                twinID = "twinID",
                                zygosity = "zygosity",
-                               sex = "sex"
+                               sex = "sex",
+                               verbose = FALSE
 ) {
+  if (verbose == TRUE) {
+    message("Restoring original column names...")
+  }
+  if (!inherits(ped, "data.frame")) {
+    stop("ped should be a data.frame or inherit to a data.frame")
+  }
+  if (!is.null(personID) && !is.null(ped$ID)) {
+    names(ped)[names(ped) == "ID"] <- personID
+  }
+  if (!is.null(momID) && !is.null(ped$momID)) {
+    names(ped)[names(ped) == "momID"] <- momID
+  }
+  if (!is.null(dadID) && !is.null(ped$dadID)) {
+    names(ped)[names(ped) == "dadID"] <- dadID
+  }
 
-  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
+  if (!is.null(famID) && !is.null(ped$famID)) {
+    names(ped)[names(ped) == "famID"] <- famID
+  }
+  if (!is.null(gen) && !is.null(ped$gen)) {
+    names(ped)[names(ped) == "gen"] <- gen
+  }
+  if (!is.null(patID) && !is.null(ped$patID)) {
+    names(ped)[names(ped) == "patID"] <- patID
+  }
+  if (!is.null(matID) && !is.null(ped$matID)) {
+    names(ped)[names(ped) == "matID"] <- matID
+  }
+  if (!is.null(spID) && !is.null(ped$spID)) {
+    names(ped)[names(ped) == "spID"] <- spID
+  }
+  if (!is.null(twinID) && !is.null(ped$twinID)) {
+    names(ped)[names(ped) == "twinID"] <- twinID
+  }
+  if (!is.null(zygosity) && !is.null(ped$zygosity)) {
+    names(ped)[names(ped) == "zygosity"] <- zygosity
+  }
+  if (!is.null(sex) && !is.null(ped$sex)) {
+    names(ped)[names(ped) == "sex"] <- sex
+  }
   ped
 }
 
diff --git a/man/addIfAny.Rd b/man/addIfAny.Rd
new file mode 100644
index 00000000..6d57a15d
--- /dev/null
+++ b/man/addIfAny.Rd
@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpChecks.R
+\name{addIfAny}
+\alias{addIfAny}
+\title{Helper function to conditionally add elements to a list}
+\usage{
+addIfAny(validation, name, value)
+}
+\arguments{
+\item{validation}{A list to which elements may be added.}
+
+\item{name}{A character string representing the name of the element to add.}
+
+\item{value}{The value to add to the list if it is not NULL or empty}
+}
+\value{
+The updated list with the new element added if applicable.
+}
+\description{
+Helper function to conditionally add elements to a list
+}
+\keyword{internal}
diff --git a/man/dropIdenticalDuplicateIDs.Rd b/man/dropIdenticalDuplicateIDs.Rd
new file mode 100644
index 00000000..a383a736
--- /dev/null
+++ b/man/dropIdenticalDuplicateIDs.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpChecks.R
+\name{dropIdenticalDuplicateIDs}
+\alias{dropIdenticalDuplicateIDs}
+\title{Drop Identical Duplicate IDs from Pedigree Data Frame}
+\usage{
+dropIdenticalDuplicateIDs(ped, ids, changes = NULL)
+}
+\arguments{
+\item{ped}{A data frame representing the pedigree.}
+
+\item{ids}{A vector of IDs to check for duplicates in the pedigree.}
+}
+\description{
+#' This function identifies and removes duplicate entries in a pedigree data frame
+based on a list of specified IDs. If multiple rows share the same ID and are
+identical, only one instance is retained. The function returns the modified pedigree
+data frame along with a log of changes made.
+}
diff --git a/man/insertEven.Rd b/man/insertEven.Rd
index 7fc08138..324e910e 100644
--- a/man/insertEven.Rd
+++ b/man/insertEven.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/insertEven.R
+% Please edit documentation in R/helpInsertEven.R
 \name{insertEven}
 \alias{insertEven}
 \alias{evenInsert}
diff --git a/man/restorePedColnames.Rd b/man/restorePedColnames.Rd
new file mode 100644
index 00000000..16a10f44
--- /dev/null
+++ b/man/restorePedColnames.Rd
@@ -0,0 +1,55 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helpNames.R
+\name{restorePedColnames}
+\alias{restorePedColnames}
+\title{Restore Original Column Names in a Pedigree Dataframe}
+\usage{
+restorePedColnames(
+  ped,
+  famID = "famID",
+  personID = "ID",
+  momID = "momID",
+  dadID = "dadID",
+  gen = "gen",
+  patID = "patID",
+  matID = "matID",
+  spID = "spID",
+  twinID = "twinID",
+  zygosity = "zygosity",
+  sex = "sex"
+)
+}
+\arguments{
+\item{ped}{A pedigree dataframe with standardized column names.}
+
+\item{famID}{The original name for the family ID column. Default is "fam
+ID".}
+
+\item{personID}{The original name for the person ID column. Default is "ID".}
+
+\item{momID}{The original name for the mother ID column. Default is "momID".}
+
+\item{dadID}{The original name for the father ID column. Default is "dadID".}
+
+\item{gen}{The original name for the generation column. Default is "gen".}
+
+\item{patID}{The original name for the paternal ID column. Default is "patID".}
+
+\item{matID}{The original name for the maternal ID column. Default is "matID".}
+
+\item{spID}{The original name for the spouse ID column. Default is "spID".}
+
+\item{twinID}{The original name for the twin ID column. Default is "twinID".}
+
+\item{zygosity}{The original name for the zygosity column. Default is "zygosity".}
+
+\item{sex}{The original name for the sex column. Default is "sex".}
+}
+\value{
+A pedigree dataframe with restored original column names.
+}
+\description{
+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.
+}
diff --git a/man/standardizeColnames.Rd b/man/standardizeColnames.Rd
index 96e3c5d0..46b2e1b4 100644
--- a/man/standardizeColnames.Rd
+++ b/man/standardizeColnames.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/cleanPedigree.R
+% Please edit documentation in R/helpNames.R
 \name{standardizeColnames}
 \alias{standardizeColnames}
 \title{Standardize Column Names in a Dataframe (Internal)}

From c0e758113ebf06964d84c343a332690dce192964 Mon Sep 17 00:00:00 2001
From: Mason Garrison <6001608+smasongarrison@users.noreply.github.com>
Date: Thu, 29 Jan 2026 14:57:19 -0500
Subject: [PATCH 3/6] Fix edge direction in ped2graph and update docs

Corrects the direction of edges in the ped2graph function to be parent-to-child for igraph compatibility. Also updates documentation for dropIdenticalDuplicateIDs and restorePedColnames to reflect new or clarified arguments.
---
 R/segmentPedigree.R              | 17 +++++++++--------
 man/dropIdenticalDuplicateIDs.Rd |  2 ++
 man/restorePedColnames.Rd        |  3 ++-
 3 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/R/segmentPedigree.R b/R/segmentPedigree.R
index 2fbf3e44..3179dbfd 100644
--- a/R/segmentPedigree.R
+++ b/R/segmentPedigree.R
@@ -139,12 +139,13 @@ ped2graph <- function(ped,
     )
     edges <- rbind(
       as.matrix(data.frame(
-        personID = as.character(ped[[personID]]),
-        momID = as.character(ped[[momID]])
+        # need to be parent to child for igraph
+        momID = as.character(ped[[momID]]),
+        personID = as.character(ped[[personID]])
       )),
       as.matrix(data.frame(
-        personID = as.character(ped[[personID]]),
-        dadID = as.character(ped[[dadID]])
+        dadID = as.character(ped[[dadID]]),
+        personID = as.character(ped[[personID]])
       ))
     )
   } else if (adjacent == "mothers") {
@@ -154,8 +155,8 @@ ped2graph <- function(ped,
       )
     )
     edges <- as.matrix(data.frame(
-      personID = as.character(ped[[personID]]),
-      momID = as.character(ped[[momID]])
+      momID = as.character(ped[[momID]]),
+      personID = as.character(ped[[personID]])
     ))
   } else if (adjacent == "fathers") {
     nodes <- unique(
@@ -164,8 +165,8 @@ ped2graph <- function(ped,
       )
     )
     edges <- as.matrix(data.frame(
-      personID = as.character(ped[[personID]]),
-      dadID = as.character(ped[[dadID]])
+      dadID = as.character(ped[[dadID]]),
+      personID = as.character(ped[[personID]])
     ))
   }
   edges <- edges[stats::complete.cases(edges), ]
diff --git a/man/dropIdenticalDuplicateIDs.Rd b/man/dropIdenticalDuplicateIDs.Rd
index a383a736..b084fe64 100644
--- a/man/dropIdenticalDuplicateIDs.Rd
+++ b/man/dropIdenticalDuplicateIDs.Rd
@@ -10,6 +10,8 @@ dropIdenticalDuplicateIDs(ped, ids, changes = NULL)
 \item{ped}{A data frame representing the pedigree.}
 
 \item{ids}{A vector of IDs to check for duplicates in the pedigree.}
+
+\item{changes}{An optional list to log changes made during the process.}
 }
 \description{
 #' This function identifies and removes duplicate entries in a pedigree data frame
diff --git a/man/restorePedColnames.Rd b/man/restorePedColnames.Rd
index 16a10f44..21a217e7 100644
--- a/man/restorePedColnames.Rd
+++ b/man/restorePedColnames.Rd
@@ -16,7 +16,8 @@ restorePedColnames(
   spID = "spID",
   twinID = "twinID",
   zygosity = "zygosity",
-  sex = "sex"
+  sex = "sex",
+  verbose = FALSE
 )
 }
 \arguments{

From bc661a3ec3fb54b1737ef0188e5eec802e432ee5 Mon Sep 17 00:00:00 2001
From: Mason Garrison <6001608+smasongarrison@users.noreply.github.com>
Date: Thu, 29 Jan 2026 16:02:03 -0500
Subject: [PATCH 4/6] Update test-segmentPedigree.R

---
 NEWS.md                               |  1 +
 tests/testthat/test-segmentPedigree.R | 24 ++++++++++++++++++++++++
 2 files changed, 25 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 2a3c973f..b6081422 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,7 @@
 # Development version: 1.6.0.9000
 
 * Add helper functions for checkParents etc
+* fixed incorrect direction so that parents are pointing to children in the graphs
 
 # BGmisc 1.6
 * Optimize  simulatePedigree and helpers for speed and memory usage
diff --git a/tests/testthat/test-segmentPedigree.R b/tests/testthat/test-segmentPedigree.R
index bd2ad541..c7224c6d 100644
--- a/tests/testthat/test-segmentPedigree.R
+++ b/tests/testthat/test-segmentPedigree.R
@@ -46,6 +46,8 @@ test_that("ped2graph produces a graph for hazard data with mothers", {
   expect_true(inherits(g, "igraph"))
 })
 
+
+
 test_that("ped2graph produces a graph for hazard data with fathers", {
   expect_silent(data(hazard))
   g <- ped2graph(hazard, adjacent = "fathers")
@@ -57,3 +59,25 @@ test_that("ped2graph produces a graph for inbreeding data", {
   g <- ped2graph(inbreeding)
   expect_true(inherits(g, "igraph"))
 })
+
+# are parents pointing to children?
+test_that("ped2graph produces correct edges for potter data", {
+  expect_silent(data(potter))
+  potter_df <- potter
+  potter_df$ID <- potter$personID
+  g <- ped2graph(potter_df)
+  expect_true(inherits(g, "igraph"))
+  vertices_df <- igraph::V(g)
+  expect_all_true(igraph::as_ids(vertices_df) %in% as.character(potter_df$personID))
+  edges_df <- igraph::E(g)
+  # are all edges from parent to child?
+  expect_all_true(
+    igraph::as_ids(edges_df) %in% paste0(potter_df$dadID, "|", potter_df$personID) |
+      igraph::as_ids(edges_df) %in% paste0(potter_df$momID, "|", potter_df$personID)
+  )
+  # are there any edges from child to parent?
+  expect_all_false(
+    igraph::as_ids(edges_df) %in% paste0(potter_df$personID, "|", potter_df$dadID) |
+      igraph::as_ids(edges_df) %in% paste0(potter_df$personID, "|", potter_df$momID)
+  )
+})

From 6ac010fd4d47bb9d8bf6d58e0a13480cc454e787 Mon Sep 17 00:00:00 2001
From: Mason Garrison <6001608+smasongarrison@users.noreply.github.com>
Date: Thu, 29 Jan 2026 16:42:16 -0500
Subject: [PATCH 5/6] add docs

---
 R/helpNames.R             | 5 ++---
 man/restorePedColnames.Rd | 2 ++
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/helpNames.R b/R/helpNames.R
index 9ef3c674..71b0cb69 100644
--- a/R/helpNames.R
+++ b/R/helpNames.R
@@ -59,6 +59,7 @@ standardizeColnames <- function(df, verbose = FALSE) {
 #' @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".
+#' @param verbose A logical indicating whether to print progress messages.
 #' @return A pedigree dataframe with restored original column names.
 restorePedColnames <- function(ped,
                                famID = "famID",
@@ -72,8 +73,7 @@ restorePedColnames <- function(ped,
                                twinID = "twinID",
                                zygosity = "zygosity",
                                sex = "sex",
-                               verbose = FALSE
-) {
+                               verbose = FALSE) {
   if (verbose == TRUE) {
     message("Restoring original column names...")
   }
@@ -118,7 +118,6 @@ restorePedColnames <- function(ped,
 }
 
 
-
 # Repair Pedigree
 #
 # This function applies a list of repair functions sequentially to a pedigree.
diff --git a/man/restorePedColnames.Rd b/man/restorePedColnames.Rd
index 21a217e7..352f9c2a 100644
--- a/man/restorePedColnames.Rd
+++ b/man/restorePedColnames.Rd
@@ -45,6 +45,8 @@ ID".}
 \item{zygosity}{The original name for the zygosity column. Default is "zygosity".}
 
 \item{sex}{The original name for the sex column. Default is "sex".}
+
+\item{verbose}{A logical indicating whether to print progress messages.}
 }
 \value{
 A pedigree dataframe with restored original column names.

From a8ef38d8307f80b44ba994a4bb175aafb5bfd685 Mon Sep 17 00:00:00 2001
From: Mason Garrison <6001608+smasongarrison@users.noreply.github.com>
Date: Thu, 29 Jan 2026 16:52:43 -0500
Subject: [PATCH 6/6] Bump version to 1.6.0.1 and update NEWS

Updated the package version in DESCRIPTION to 1.6.0.1 and added a corresponding entry in NEWS.md to reflect recent changes and improvements.
---
 DESCRIPTION | 2 +-
 NEWS.md     | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 69a4f50f..2d27bf2f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: BGmisc
 Title: An R Package for Extended Behavior Genetics Analysis
-Version: 1.6.0
+Version: 1.6.0.1
 Authors@R: c(
     person("S. Mason", "Garrison", , "garrissm@wfu.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4804-6003")),
diff --git a/NEWS.md b/NEWS.md
index b6081422..92292f4a 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,10 +1,9 @@
 # BGmisc NEWS
 # Development version: 1.6.0.9000
 
+# BGmisc 1.6.0.1
 * Add helper functions for checkParents etc
 * fixed incorrect direction so that parents are pointing to children in the graphs
-
-# BGmisc 1.6
 * Optimize  simulatePedigree and helpers for speed and memory usage
 * Major gains in speed for deeper pedigrees
 * Added more tests for simulatePedigree