Added computeAllFreqs2 function

R/admix1.R

@@ -401,29 +401,3 @@ admix1 <- function(tietue) {
 # global SUMCOUNTS; SUMCOUNTS = [];
 # global PARTITION; PARTITION = [];
 # global POP_LOGML; POP_LOGML = [];
-
-# %--------------------------------------------------------
-
-
-# function allFreqs = computeAllFreqs2(noalle)
-# % Lisää a priori jokaista alleelia
-# % joka populaation joka lokukseen j 1/noalle(j) verran.
-
-# global COUNTS;
-# global SUMCOUNTS;
-
-# max_noalle = size(COUNTS,1);
-# nloci = size(COUNTS,2);
-# npops = size(COUNTS,3);
-
-# sumCounts = SUMCOUNTS+ones(size(SUMCOUNTS));
-# sumCounts = reshape(sumCounts', [1, nloci, npops]);
-# sumCounts = repmat(sumCounts, [max_noalle, 1 1]);
-
-# 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 = counts./sumCounts;

R/computeAllFreqs2.R

@@ -0,0 +1,23 @@
+#' @title Compute all freqs - version 2
+#' @description Lisää a priori jokaista alleelia joka populaation joka lokukseen
+#' j 1/noalle(j) verran.
+computeAllFreqs2 <- function (noalle, COUNTS = matrix(NA, 0, 0),
+    SUMCOUNTS = sum(COUNTS)) {
+
+    max_noalle <- size(COUNTS, 1)
+    nloci <- size(COUNTS,2)
+    npops <- size(COUNTS,3)
+
+    sumCounts <- SUMCOUNTS + ones(size(SUMCOUNTS))
+    sumCounts <- reshape(t(sumCounts), c(1, nloci, npops))
+    sumCounts <- repmat(sumCounts, c(max_noalle, 1, 1))
+
+    prioriAlleelit <- zeros(max_noalle, nloci)
+    for (j in 1:nloci) {
+         prioriAlleelit[1:noalle[j], j] <- 1 / noalle[j]
+    }
+    prioriAlleelit <- repmat(prioriAlleelit, c(1, 1, npops))
+    counts <- COUNTS + prioriAlleelit
+    allFreqs <- counts / sumCounts
+    return(allFreqs)
+}

man/computeAllFreqs2.Rd

@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/computeAllFreqs2.R
+\name{computeAllFreqs2}
+\alias{computeAllFreqs2}
+\title{Compute all freqs - version 2}
+\usage{
+computeAllFreqs2(noalle, COUNTS = matrix(NA, 0, 0), SUMCOUNTS = sum(COUNTS))
+}
+\description{
+Lisää a priori jokaista alleelia joka populaation joka lokukseen
+j 1/noalle(j) verran.
+}