Merge pull request #45 from R-Computing-Lab/readgedcom

Readgedcom

Author: smasongarrison

R/buildPedigree.R

@@ -177,7 +177,7 @@ ped2graph <- function(ped,
 #' @export
 #'
 ped2maternal <- function(ped, personID = "ID",
-                         momID = "momID", dadID = "dadID", matID = "matID",...) {
+                         momID = "momID", dadID = "dadID", matID = "matID", ...) {
   # Call to wrapper function
   .ped2id(ped = ped, personID = personID, momID = momID, dadID = dadID, famID = matID, type = "mothers")
 }
@@ -197,7 +197,7 @@ ped2maternal <- function(ped, personID = "ID",
 #'
 ped2paternal <- function(ped, personID = "ID",
                          momID = "momID", dadID = "dadID",
-                         patID = "patID",...) {
+                         patID = "patID", ...) {
   # Call to wrapper function
   .ped2id(ped = ped, personID = personID, momID = momID, dadID = dadID, famID = patID, type = "fathers")
 }

R/checkIDs.R

@@ -76,26 +76,26 @@ checkIDs <- function(ped, verbose = FALSE, repair = FALSE) {
       ))
     }
     validation_results$within_row_duplicates <- TRUE
- if(validation_results$total_own_father > 0){
-     validation_results$is_own_father_ids <- unique(is_own_father)
+    if (validation_results$total_own_father > 0) {
+      validation_results$is_own_father_ids <- unique(is_own_father)
       if (verbose) {
         cat(paste0(
           validation_results$total_own_father,
           " individuals are their own fathers.\n"
         ))
       }
     }
-if(validation_results$total_own_mother > 0){
-     validation_results$is_own_mother_ids <- unique(is_own_mother)
+    if (validation_results$total_own_mother > 0) {
+      validation_results$is_own_mother_ids <- unique(is_own_mother)
       if (verbose) {
         cat(paste0(
           validation_results$total_own_mother,
           " individuals are their own mothers.\n"
         ))
       }
     }
-if(validation_results$total_duplicated_parents > 0){
-     validation_results$duplicated_parents_ids <- unique(duplicated_parents)
+    if (validation_results$total_duplicated_parents > 0) {
+      validation_results$duplicated_parents_ids <- unique(duplicated_parents)
       if (verbose) {
         cat(paste0(
           validation_results$total_duplicated_parents,

R/computeRelatedness.R

@@ -59,7 +59,7 @@ calculateRelatedness <- function(
     denom_emp <- denom_m * total_m * weight_m + total_a * weight_a
     if (denom_emp == 0) stop("Denominator in empirical adjustment is zero.")
 
-    coef <- (coef * total_a * weight_a + maternal * total_m * weight_m)/denom_emp
+    coef <- (coef * total_a * weight_a + maternal * total_m * weight_m) / denom_emp
   }
   return(coef)
 }