Implemented simulateIndividuals

R/admix1.R

@@ -453,29 +453,4 @@ admix1 <- function(tietue) {
 #         simuloidut = randdir(counts(1:noalle(j),j,i) , noalle(j));
 #         allfreqs(1:noalle(j),j,i) = simuloidut;
 #     end
-# end
-
-# %--------------------------------------------------------------------------
-
-
-# function refData = simulateIndividuals(n,rowsFromInd,allfreqs,pop, missing_level)
-# % simulate n individuals from population pop, such that approximately
-# % proportion "missing_level" of the alleles are present. 
-
-# nloci = size(allfreqs,2);
-
-# refData = zeros(n*rowsFromInd,nloci);
-# counter = 1;  % which row will be generated next.
-
-# for ind = 1:n
-#     for loc = 1:nloci
-#         for k=0:rowsFromInd-1
-#             if rand<missing_level
-#                 refData(counter+k,loc) = simuloiAlleeli(allfreqs,pop,loc);
-#             else
-#                 refData(counter+k,loc) = -999;
-#             end
-#         end
-#     end
-#     counter = counter+rowsFromInd;
 # end

R/simulateIndividuals.R

@@ -0,0 +1,27 @@
+#' @title Simulate individuals
+#' @description simulate n individuals from population pop, such that
+#' proportion "missing_level" of the alleles are present. 
+#' @export
+
+simulateIndividuals <- function(n, rowsFromInd, allfreqs, pop, missing_level) {
+    nloci <- size(allfreqs, 2)
+
+    refData <- zeros(n * rowsFromInd, nloci)
+    counter <- 1 # which row will be generated next.
+
+    for (ind in 1:n) {
+        for (loc in 1:nloci) {
+            for (k in 0:(rowsFromInd - 1)) {
+                if (runif(1) < missing_level) {
+                    refData[counter + k, loc] <- simuloiAlleeli(
+                        allfreqs, pop, loc
+                    )
+                } else {
+                    refData[counter + k, loc] <- -999
+                }
+            }
+        }
+        counter <- counter + rowsFromInd
+    }
+    return(refData)
+}