From 2e8ad9a89d6b4ab9570b11ae9c31c866341eeff6 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <waldir.leoncio@gmail.com>
Date: Thu, 30 Jan 2020 16:20:36 +0100
Subject: [PATCH] Implemented simulateIndividuals

---
 NAMESPACE                    |  1 +
 R/admix1.R                   | 25 -------------------------
 R/simulateIndividuals.R      | 27 +++++++++++++++++++++++++++
 man/simulateIndividuals.Rd   | 12 ++++++++++++
 tests/testthat/test-admix1.R | 20 ++++++++++++++++++++
 5 files changed, 60 insertions(+), 25 deletions(-)
 create mode 100644 R/simulateIndividuals.R
 create mode 100644 man/simulateIndividuals.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 79a2e2f..f49f1d9 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,6 +14,7 @@ export(proportion2str)
 export(rand)
 export(randdir)
 export(repmat)
+export(simulateIndividuals)
 export(simuloiAlleeli)
 export(suoritaMuutos)
 export(times)
diff --git a/R/admix1.R b/R/admix1.R
index d611540..8251e22 100644
--- a/R/admix1.R
+++ b/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
\ No newline at end of file
diff --git a/R/simulateIndividuals.R b/R/simulateIndividuals.R
new file mode 100644
index 0000000..e6326d4
--- /dev/null
+++ b/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)
+}
\ No newline at end of file
diff --git a/man/simulateIndividuals.Rd b/man/simulateIndividuals.Rd
new file mode 100644
index 0000000..782cdd9
--- /dev/null
+++ b/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.
+}
diff --git a/tests/testthat/test-admix1.R b/tests/testthat/test-admix1.R
index 41cb3f4..962dcdf 100644
--- a/tests/testthat/test-admix1.R
+++ b/tests/testthat/test-admix1.R
@@ -189,4 +189,24 @@ test_that("simuloiAlleeli works like on Matlab", {
     expect_equal(simuloiAlleeli(ra1, 2, 1), 1)
     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
+    )
 })
\ No newline at end of file