add number of loci to gl.report.heterozygosity method "ind"

green-striped-gecko · Feb 5, 2024 · 00fa98b · 00fa98b
1 parent f5637d2
commit 00fa98b
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/R/gl.report.heterozygosity.r b/R/gl.report.heterozygosity.r
@@ -1074,6 +1074,8 @@ gl.report.heterozygosity <- function(x,
     c.hets <- array(NA, nInd(x))
     c.hom0 <- array(NA, nInd(x))
     c.hom2 <- array(NA, nInd(x))
+    c.nloc <- array(NA, nInd(x))
+
     for (i in 1:nInd(x)) {
       c.na[i] <- sum(is.na(m[i, ]))
       c.hets[i] <-
@@ -1082,13 +1084,14 @@ gl.report.heterozygosity <- function(x,
         sum(m[i, ] == 0, na.rm = TRUE) / (nLoc(x) - c.na[i])
       c.hom2[i] <-
         sum(m[i, ] == 2, na.rm = TRUE) / (nLoc(x) - c.na[i])
+      c.nloc[i] <- (nLoc(x) - c.na[i])
     }
 
     # Join the sample sizes with the heterozygosities
     df <-
-      cbind.data.frame(x@ind.names, c.hets, c.hom0, c.hom2)
+      cbind.data.frame(x@ind.names, c.hets, c.hom0, c.hom2,c.nloc)
     names(df) <-
-      c("ind.name", "Ho", "f.hom.ref", "f.hom.alt")
+      c("ind.name", "Ho", "f.hom.ref", "f.hom.alt","n.Loc")
 
     # Boxplot
     if (plot.display) {