From eff04b312442480a98b50bca727aca3f07e248e5 Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <waldir.leoncio@gmail.com>
Date: Tue, 25 Feb 2020 15:41:05 +0100
Subject: [PATCH] Added poistaLiianPienet

---
 NAMESPACE                    |  1 +
 R/poistaLiianPienet.R        | 49 ++++++++++++++++++++++++++++++++++++
 man/poistaLiianPienet.Rd     | 27 ++++++++++++++++++++
 tests/testthat/test-admix1.R |  5 ++++
 4 files changed, 82 insertions(+)
 create mode 100644 R/poistaLiianPienet.R
 create mode 100644 man/poistaLiianPienet.Rd

diff --git a/NAMESPACE b/NAMESPACE
index c80ce2b..aa5e19f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,6 +11,7 @@ export(etsiParas)
 export(laskeMuutokset4)
 export(learn_simple_partition)
 export(ownNum2Str)
+export(poistaLiianPienet)
 export(proportion2str)
 export(rand)
 export(randdir)
diff --git a/R/poistaLiianPienet.R b/R/poistaLiianPienet.R
new file mode 100644
index 0000000..685a8f1
--- /dev/null
+++ b/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)
+}
\ No newline at end of file
diff --git a/man/poistaLiianPienet.Rd b/man/poistaLiianPienet.Rd
new file mode 100644
index 0000000..1e48921
--- /dev/null
+++ b/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?
+}
diff --git a/tests/testthat/test-admix1.R b/tests/testthat/test-admix1.R
index 12ae460..453a1e1 100644
--- a/tests/testthat/test-admix1.R
+++ b/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)
 })
\ No newline at end of file