From 1ac54301a60d71a7fa52bdfe265f0811a2f3bc58 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <waldir.leoncio@gmail.com>
Date: Thu, 30 Jan 2020 17:19:10 +0100
Subject: [PATCH] Adde basic elements of simulateAllFreqs

---
 NAMESPACE               |  1 +
 R/admix1.R              | 29 +----------------------------
 R/simulateAllFreqs.R    | 28 ++++++++++++++++++++++++++++
 man/simulateAllFreqs.Rd | 17 +++++++++++++++++
 4 files changed, 47 insertions(+), 28 deletions(-)
 create mode 100644 R/simulateAllFreqs.R
 create mode 100644 man/simulateAllFreqs.Rd

diff --git a/NAMESPACE b/NAMESPACE
index f49f1d9..673ff82 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,6 +14,7 @@ export(proportion2str)
 export(rand)
 export(randdir)
 export(repmat)
+export(simulateAllFreqs)
 export(simulateIndividuals)
 export(simuloiAlleeli)
 export(suoritaMuutos)
diff --git a/R/admix1.R b/R/admix1.R
index 8251e22..28ce731 100644
--- a/R/admix1.R
+++ b/R/admix1.R
@@ -426,31 +426,4 @@ admix1 <- function(tietue) {
 # end
 # prioriAlleelit = repmat(prioriAlleelit, [1,1,npops]);
 # counts = COUNTS + prioriAlleelit;
-# allFreqs = counts./sumCounts;
-
-
-# function allfreqs = simulateAllFreqs(noalle)
-# % Lisää jokaista alleelia joka populaation joka lokukseen j 1/noalle(j)
-# % verran. Näin saatuja counts:eja vastaavista Dirichlet-jakaumista
-# % simuloidaan arvot populaatioiden alleelifrekvensseille.
-
-# global COUNTS;
-
-# max_noalle = size(COUNTS,1);
-# nloci = size(COUNTS,2);
-# npops = size(COUNTS,3);
-
-# prioriAlleelit = zeros(max_noalle,nloci);
-# for j=1:nloci
-#     prioriAlleelit(1:noalle(j),j) = 1/noalle(j);
-# end
-# prioriAlleelit = repmat(prioriAlleelit, [1,1,npops]);
-# counts = COUNTS + prioriAlleelit;
-# allfreqs = zeros(size(counts));
-
-# for i=1:npops
-#     for j=1:nloci
-#         simuloidut = randdir(counts(1:noalle(j),j,i) , noalle(j));
-#         allfreqs(1:noalle(j),j,i) = simuloidut;
-#     end
-# end
\ No newline at end of file
+# allFreqs = counts./sumCounts;
\ No newline at end of file
diff --git a/R/simulateAllFreqs.R b/R/simulateAllFreqs.R
new file mode 100644
index 0000000..3a747e5
--- /dev/null
+++ b/R/simulateAllFreqs.R
@@ -0,0 +1,28 @@
+#' @title Simulate All Frequencies
+#' @description Lisää jokaista alleelia joka populaation joka lokukseen j1/noalle(j) verran. Näin saatuja counts:eja vastaavista Dirichlet-jakaumista simuloidaan arvot populaatioiden alleelifrekvensseille.
+#' Add each allele to each locus in each population by j 1 / noalle(j). The Dirichlet distributions corresponding to the counts thus obtained simulate values for the allele frequencies of the populations.
+#' @param noalle noalle
+#' @param COUNTS COUNTS
+#' @export
+
+simulateAllFreqs <- function(noalle, COUNTS = matrix(0)) {
+    max_noalle <- size(COUNTS, 1)
+    nloci <- size(COUNTS, 2)
+    npops <- size(COUNTS, 3)
+
+    prioriAlleelit <- zeros(max_noalle, nloci)
+    for (j in 1:nloci) {
+        prioriAlleelit[1:noalle[j], j] <- 1 / noalle[j]
+    }
+    prioriAlleelit <- repmat(prioriAlleelit, matrix(c(1, 1, npops), ncol = 1))
+    counts <- COUNTS + prioriAlleelit
+    allfreqs <- zeros(size(counts))
+
+    for (i in 1:npops) {
+        for (j in 1:nloci) {
+            simuloidut <- randdir(counts[1:noalle[j], j, i] , noalle[j])
+            allfreqs[1:noalle[j], j, i] <- simuloidut
+        }
+    }
+    return(allfreqs)
+}
\ No newline at end of file
diff --git a/man/simulateAllFreqs.Rd b/man/simulateAllFreqs.Rd
new file mode 100644
index 0000000..463ef80
--- /dev/null
+++ b/man/simulateAllFreqs.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/simulateAllFreqs.R
+\name{simulateAllFreqs}
+\alias{simulateAllFreqs}
+\title{Simulate All Frequencies}
+\usage{
+simulateAllFreqs(noalle, COUNTS = matrix(0))
+}
+\arguments{
+\item{noalle}{noalle}
+
+\item{COUNTS}{COUNTS}
+}
+\description{
+Lisää jokaista alleelia joka populaation joka lokukseen j1/noalle(j) verran. Näin saatuja counts:eja vastaavista Dirichlet-jakaumista simuloidaan arvot populaatioiden alleelifrekvensseille.
+Add each allele to each locus in each population by j 1 / noalle(j). The Dirichlet distributions corresponding to the counts thus obtained simulate values for the allele frequencies of the populations.
+}