Merge pull request #111 from AudreyAAMartin/patch-1

Fix to issue 110 (sortPed)
gaynorr · Feb 9, 2023 · 6bf1b1d · 6bf1b1d
2 parents d5dff24 + 2215f29
commit 6bf1b1d
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/R/crossing.R b/R/crossing.R
@@ -663,24 +663,24 @@ sortPed = function(id, mother, father, maxCycle=100){
     for(i in which(unsorted)){
       if(is.na(output$mother[i])&is.na(output$father[i])){
         # Is a founder
-        output$gen[i] = gen
+        output$gen[i] = 1
         unsorted[i] = FALSE
       }else if(is.na(output$mother[i])){
         # Mother is a founder
         if(!unsorted[output$father[i]]){
-          output$gen[i] = gen
+          output$gen[i] = output$gen[output$father[i]] + 1
           unsorted[i] = FALSE
         }
       }else if(is.na(output$father[i])){
         # Father is a founder
         if(!unsorted[output$mother[i]]){
-          output$gen[i] = gen
+          output$gen[i] = output$gen[output$mother[i]] + 1
           unsorted[i] = FALSE
         }
       }else{
         # Both parents are in the pedigree
         if(!unsorted[output$mother[i]] & !unsorted[output$father[i]]){
-          output$gen[i] = gen
+          output$gen[i] = pmax(output$gen[output$mother[i]], output$gen[output$father[i]]) + 1
           unsorted[i] = FALSE
         }
       }