Implemented simulateIndividuals

NAMESPACE

@@ -14,6 +14,7 @@ export(proportion2str)
 export(rand)
 export(randdir)
 export(repmat)
+export(simulateIndividuals)
 export(simuloiAlleeli)
 export(suoritaMuutos)
 export(times)

R/admix1.R

@@ -454,28 +454,3 @@ admix1 <- function(tietue) {
 #         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)
+}

man/simulateIndividuals.Rd

@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/simulateIndividuals.R
+\name{simulateIndividuals}
+\alias{simulateIndividuals}
+\title{Simulate individuals}
+\usage{
+simulateIndividuals(n, rowsFromInd, allfreqs, pop, missing_level)
+}
+\description{
+simulate n individuals from population pop, such that
+proportion "missing_level" of the alleles are present.
+}

tests/testthat/test-admix1.R

@@ -190,3 +190,23 @@ test_that("simuloiAlleeli works like on Matlab", {
     expect_equal(simuloiAlleeli(mx1, 1, 2), 2)
     expect_equal(simuloiAlleeli(mx2, 1, 3), 1)
 })
+
+test_that("simulateIndividuals works like on Matlab", {
+    expect_equal(
+        object = simulateIndividuals(1, 3, 2, 0, .1),
+        expected = matrix(rep(-999, 3), 3)
+    )
+    expect_equal(
+        object = simulateIndividuals(5, 3, 1:3, 4, 0),
+        expected = matrix(rep(-999, 15 * 3), 15)
+    )
+    expect_equal(
+        object = simulateIndividuals(3, 3, 2, 1, 1),
+        expected = matrix(rep(1, 9), 9)
+    )
+    set.seed(2)
+    expect_equal(
+        object = sum(simulateIndividuals(3, 3, 2, 1, .5) == 1),
+        expected = 6
+    )
+})