Added code and tests for simuloiAlleeli

NAMESPACE

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

R/admix1.R

@@ -478,12 +478,4 @@ admix1 <- function(tietue) {
 #         end
 #     end
 #     counter = counter+rowsFromInd;
-# end
+# end
-
-# function all = simuloiAlleeli(allfreqs,pop,loc)
-# % Simuloi populaation pop lokukseen loc alleelin.
-# freqs = allfreqs(:,loc,pop);
-# cumsumma = cumsum(freqs);
-# arvo = rand;
-# isommat = find(cumsumma>arvo);
-# all = min(isommat);

R/simuloiAlleeli.R

@@ -0,0 +1,17 @@
+#' @title simuloiAlleeli
+#' @description Simuloi populaation pop lokukseen loc alleelin.
+#' @note This function is (only?) called by `simulateIndividuals()`. Therefore, exporting it is probably unnecessary.
+#' @export
+
+simuloiAlleeli <- function(allfreqs, pop, loc) {
+    if (length(dim(allfreqs)) == 3) { # distinguish between arrays and matrices
+        freqs <- allfreqs[, loc, pop]
+    } else {
+        freqs <- allfreqs[, loc]
+    }
+    cumsumma <- cumsum(freqs)
+    arvo <- runif(1)
+    isommat <- which(cumsumma > arvo)
+    all <- min(isommat)
+    return(all)
+}

man/simuloiAlleeli.Rd

@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/simuloiAlleeli.R
+\name{simuloiAlleeli}
+\alias{simuloiAlleeli}
+\title{simuloiAlleeli}
+\usage{
+simuloiAlleeli(allfreqs, pop, loc)
+}
+\description{
+Simuloi populaation pop lokukseen loc alleelin.
+}
+\note{
+This function is (only?) called by `simulateIndividuals()`. Therefore, exporting it is probably unnecessary.
+}

tests/testthat/test-admix1.R

@@ -179,4 +179,14 @@ test_that("computePersonalAllFreqs works like on Matlab", {
     expect_equal(computePersonalAllFreqs(1, 1:4, mx, 1), c(15, 40))
     expect_equal(computePersonalAllFreqs(1, 1:3, mx, 1), c(15, 40))
     expect_equal(computePersonalAllFreqs(1, 1:2, mx, 1), c(15, 40))
+})
+
+test_that("simuloiAlleeli works like on Matlab", {
+    # TODO: test on vector
+    ra1 <- array(1:12, c(2, 2, 3))
+    mx1 <- matrix(c(3, 5, 0, 9), 2)
+    mx2 <- matrix(c(3, 5, 0, 9, 5, 8), 2)
+    expect_equal(simuloiAlleeli(ra1, 2, 1), 1)
+    expect_equal(simuloiAlleeli(mx1, 1, 2), 2)
+    expect_equal(simuloiAlleeli(mx2, 1, 3), 1)
 })