Merge branch 'poistaLiianPienet' into dev

NAMESPACE

@@ -11,6 +11,7 @@ export(etsiParas)
 export(laskeMuutokset4)
 export(learn_simple_partition)
 export(ownNum2Str)
+export(poistaLiianPienet)
 export(proportion2str)
 export(rand)
 export(randdir)

R/admix1.R

@@ -350,54 +350,4 @@ admix1 <- function(tietue) {
 #             save([pathname filename], 'tietue', '-v7.3'); # added by Lu Cheng, 08.06.2012
 #         end
 #     end
-}
+}
-
-
-# function [npops] = poistaLiianPienet(npops, rowsFromInd, alaraja)
-# % Muokkaa tulokset muotoon, jossa outlier yksilöt on
-# % poistettu. Tarkalleen ottaen poistaa ne populaatiot,
-# % joissa on vähemmän kuin 'alaraja':n verran yksilöit?
-
-# global PARTITION;
-# global COUNTS;
-# global SUMCOUNTS;
-
-# popSize=zeros(1,npops);
-# for i=1:npops
-#     popSize(i)=length(find(PARTITION==i));
-# end
-# miniPops = find(popSize<alaraja);
-
-# if length(miniPops)==0
-#     return;
-# end
-
-# outliers = [];
-# for pop = miniPops
-#     inds = find(PARTITION==pop);
-#     disp('Removed individuals: ');
-#     disp(num2str(inds));
-#     outliers = [outliers; inds];
-# end
-
-# ninds = length(PARTITION);
-# PARTITION(outliers) = 0;
-# korit = unique(PARTITION(find(PARTITION>0)));
-# for n=1:length(korit)
-#     kori = korit(n);
-#     yksilot = find(PARTITION==kori);
-#     PARTITION(yksilot) = n;
-# end
-# COUNTS(:,:,miniPops) = [];
-# SUMCOUNTS(miniPops,:) = [];
-
-# npops = npops-length(miniPops);
-
-# %------------------------------------------------------------------------
-
-# function clearGlobalVars
-
-# global COUNTS; COUNTS = [];
-# global SUMCOUNTS; SUMCOUNTS = [];
-# global PARTITION; PARTITION = [];
-# global POP_LOGML; POP_LOGML = [];

R/poistaLiianPienet.R

@@ -0,0 +1,49 @@
+#' @title Remove too small
+#' @description Muokkaa tulokset muotoon, jossa outlier yksilöt on poistettu.
+#' Tarkalleen ottaen poistaa ne populaatiot, joissa on vähemmän kuin
+#' 'alaraja':n verran yksilöit?
+#' @param npops npops
+#' @param rowsFromInd rowsFromInd
+#' @param alaraja alaraja
+#' @export
+poistaLiianPienet <- function (npops, rowsFromInd, alaraja,
+    PARTITION = matrix(NA, 0, 0), COUNTS = matrix(NA, 0, 0),
+    SUMCOUNTS = NA) {
+
+    popSize <- zeros(1,npops)
+    if (npops > 0) {
+        for (i in 1:npops) {
+            popSize[i] <- length(which(PARTITION == i))
+        }
+    }
+    miniPops <- which(popSize < alaraja)
+
+    if (length(miniPops) == 0) {
+        return(npops)
+    }
+
+    outliers <- matrix(NA, 0, 0)
+    for (pop in miniPops) {
+        inds <- which(PARTITION == pop)
+        cat('Removed individuals: ')
+        cat(as.character(inds))
+        outliers = matrix(c(outliers, inds), ncol=1)
+    }
+
+    ninds <- length(PARTITION)
+    PARTITION[outliers] <- 0
+    korit <- unique(PARTITION(which(PARTITION > 0)))
+    for (n in 1:length(korit)) {
+        kori <- korit[n]
+        yksilot <- which(PARTITION == kori)
+        PARTITION[yksilot] == n
+    }
+
+    # TODO: add COUNTS, SUMCOUNTS and PARTITION to return or use <<-
+    COUNTS[, , miniPops] <- NA
+    SUMCOUNTS[miniPops, ] <- NA
+
+    npops <- npops - length(miniPops)
+
+    return(npops)
+}

man/computeAllFreqs2.Rd

@@ -4,7 +4,7 @@
 \alias{computeAllFreqs2}
 \title{Compute all freqs - version 2}
 \usage{
-computeAllFreqs2(noalle, COUNTS = matrix(NA, 0, 0), SUMCOUNTS = sum(COUNTS))
+computeAllFreqs2(noalle, COUNTS = matrix(NA, 0, 0), SUMCOUNTS = NA)
 }
 \arguments{
 \item{noalle}{noalle}

man/poistaLiianPienet.Rd

@@ -0,0 +1,27 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/poistaLiianPienet.R
+\name{poistaLiianPienet}
+\alias{poistaLiianPienet}
+\title{Remove too small}
+\usage{
+poistaLiianPienet(
+  npops,
+  rowsFromInd,
+  alaraja,
+  PARTITION = matrix(NA, 0, 0),
+  COUNTS = matrix(NA, 0, 0),
+  SUMCOUNTS = NA
+)
+}
+\arguments{
+\item{npops}{npops}
+
+\item{rowsFromInd}{rowsFromInd}
+
+\item{alaraja}{alaraja}
+}
+\description{
+Muokkaa tulokset muotoon, jossa outlier yksilöt on poistettu.
+Tarkalleen ottaen poistaa ne populaatiot, joissa on vähemmän kuin
+'alaraja':n verran yksilöit?
+}

man/repmat.Rd

@@ -9,7 +9,8 @@ repmat(mx, n)
 \arguments{
 \item{mx}{matrix}
 
-\item{n}{either a scalar with the number of replications in both rows and columns or a 2-length vector with individual repetitions.}
+\item{n}{either a scalar with the number of replications in both rows and
+columns or a <= 3-length vector with individual repetitions.}
 }
 \value{
 matrix replicated over `ncol(mx) * n` columns and `nrow(mx) * n` rows

tests/testthat/test-admix1.R

@@ -227,4 +227,9 @@ test_that("simulateAllFreqs works as expected", {
 
 test_that("computeAllFreqs2 works as expected", {
     expect_equivalent(computeAllFreqs2(10), matrix(NA, 0, 0))
+})
+
+test_that("poistaLiianPienet works as expected", {
+    expect_equal(poistaLiianPienet(100, matrix(1:4, 2), 0), 100)
+    expect_equal(poistaLiianPienet(100, matrix(1:4, 2), -5), 100)
 })