Merge branch 'setdiff' into unite-laskeMuutokset

NAMESPACE

@@ -23,6 +23,7 @@ export(linkage)
 export(logml2String)
 export(lueGenePopData)
 export(lueNimi)
+export(max_MATLAB)
 export(min_MATLAB)
 export(noIndex)
 export(ownNum2Str)
@@ -34,6 +35,7 @@ export(randdir)
 export(repmat)
 export(rivinSisaltamienMjonojenLkm)
 export(selvitaDigitFormat)
+export(setdiff_MATLAB)
 export(simulateAllFreqs)
 export(simulateIndividuals)
 export(simuloiAlleeli)

R/addToSummary.R

@@ -1,4 +1,4 @@
-addToSummary <- funciton(logml, partitionSummary, worstIndex) {
+addToSummary <- function(logml, partitionSummary, worstIndex) {
 	# Tiedet<65><74>n, ett<74> annettu logml on isompi kuin huonoin arvo
 	# partitionSummary taulukossa. Jos partitionSummary:ss<73> ei viel<65> ole
 	# annettua logml arvoa, niin lis<69>t<EFBFBD><74>n worstIndex:in kohtaan uusi logml ja
@@ -6,13 +6,13 @@ addToSummary <- funciton(logml, partitionSummary, worstIndex) {
 
 	apu <- find(abs(partitionSummary[, 2] - logml) < 1e-5)
 	if (isempty(apu)) {
-	    # Nyt l<>ydetty partitio ei ole viel<65> kirjattuna summaryyn.
+		# Nyt l<>ydetty partitio ei ole viel<65> kirjattuna summaryyn.
-	    npops <- length(unique(PARTITION))
+		npops <- length(unique(PARTITION))
-	    partitionSummary[worstIndex, 1] <- npops
+		partitionSummary[worstIndex, 1] <- npops
-	    partitionSummary[worstIndex, 2] <- logml
+		partitionSummary[worstIndex, 2] <- logml
-	    added <- 1
+		added <- 1
 	} else {
-	    added <- 0
+		added <- 0
 	}
 	return(list(partitionSummary = partitionSummary, added = added))
 }

R/setdiff.R

@@ -0,0 +1,17 @@
+#' @title Set differences of two arrays
+#' @description Loosely replicates the behavior of the homonym Matlab function
+#' @param A first array
+#' @param B second awway
+#' @param legacy if `TRUE`, preserves the behavior of
+#' @return
+#' @author Waldir Leoncio
+#' @export
+setdiff_MATLAB <- function(A, B, legacy = FALSE) {
+	if (is(A, "numeric") & is(B, "numeric")) {
+		values <- sort(unique(A[is.na(match(A, B))]))
+	} else if (is(A, "data.frame") & is(B, "data.frame")) {
+		stop("Not implemented for data frames")
+	}
+	# TODO: add support for indices (if necessary)
+	return(values)
+}

man/admixture_initialization.Rd

@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/admixture_initialization.R
+\name{admixture_initialization}
+\alias{admixture_initialization}
+\title{Seuraavat kolme funktiota liittyvat alkupartition muodostamiseen.}
+\usage{
+admixture_initialization(data_matrix, nclusters, Z)
+}
+\description{
+Seuraavat kolme funktiota liittyvat alkupartition muodostamiseen.
+}

man/laskeMuutokset4.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/laskeMuutokset4.R
+% Please edit documentation in R/laskeMuutokset12345.R
 \name{laskeMuutokset4}
 \alias{laskeMuutokset4}
 \title{Calculate changes?}
@@ -20,6 +20,6 @@ laskeMuutokset4(osuus, osuusTaulu, omaFreqs, logml, COUNTS = matrix(0))
 \description{
 Palauttaa npops*npops taulun, jonka alkio (i,j) kertoo, mik?on
 muutos logml:ss? mikäli populaatiosta i siirretään osuuden verran
-todennäköisyysmassaa populaatioon j. Mikäli populaatiossa i ei ole mitään 
+todennäköisyysmassaa populaatioon j. Mikäli populaatiossa i ei ole mitään
 siirrettävää, on vastaavassa kohdassa rivi nollia.
 }

man/max_MATLAB.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/min_max_MATLAB.R
+\name{max_MATLAB}
+\alias{max_MATLAB}
+\title{Maximum (MATLAB version)}
+\usage{
+max_MATLAB(X, indices = TRUE)
+}
+\arguments{
+\item{X}{matrix}
+
+\item{indices}{return indices?}
+}
+\value{
+Either a list or a vector
+}
+\description{
+Finds the minimum value for each column of a matrix, potentially returning the indices instead
+}
+\author{
+Waldir Leoncio
+}

man/min_MATLAB.Rd

@@ -1,11 +1,15 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/min.R, R/min_MATLAB.R
+% Please edit documentation in R/min.R, R/min_MATLAB.R, R/min_max_MATLAB.R
 \name{min_MATLAB}
 \alias{min_MATLAB}
 \title{Minimum (MATLAB version)}
 \usage{
 min_MATLAB(X, indices = TRUE)
 
+min_MATLAB(X, indices = TRUE)
+
+min_MATLAB(X, indices = TRUE)
+
 min_MATLAB(X, indices = TRUE)
 }
 \arguments{
@@ -16,15 +20,27 @@ min_MATLAB(X, indices = TRUE)
 \value{
 Either a list or a vector
 
+Either a list or a vector
+
+Either a list or a vector
+
 Either a list or a vector
 }
 \description{
 Finds the minimum value for each column of a matrix, potentially returning the indices instead
 
+Finds the minimum value for each column of a matrix, potentially returning the indices instead
+
+Finds the minimum value for each column of a matrix, potentially returning the indices instead
+
 Finds the minimum value for each column of a matrix, potentially returning the indices instead
 }
 \author{
 Waldir Leoncio
 
+Waldir Leoncio
+
+Waldir Leoncio
+
 Waldir Leoncio
 }

man/setdiff_MATLAB.Rd

@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/setdiff.R
+\name{setdiff_MATLAB}
+\alias{setdiff_MATLAB}
+\title{Set differences of two arrays}
+\usage{
+setdiff_MATLAB(A, B, legacy = FALSE)
+}
+\arguments{
+\item{A}{first array}
+
+\item{B}{second awway}
+
+\item{legacy}{if `TRUE`, preserves the behavior of}
+}
+\value{
+
+}
+\description{
+Loosely replicates the behavior of the homonym Matlab function
+}
+\author{
+Waldir Leoncio
+}

tests/testthat/test-convertedBaseFunctions.R

@@ -158,12 +158,13 @@ test_that("find works as expected", {
 })
 
 test_that("sortrows works as expected", {
-	 mx <- matrix(c(3, 2, 2, 1, 1, 10, 0, pi), 4)
+	mx <- matrix(c(3, 2, 2, 1, 1, 10, 0, pi), 4)
-	 expect_equal(sortrows(mx), matrix(c(1, 2, 2, 3, pi, 10, 0, 1), 4))
+	expect_equal(sortrows(mx), matrix(c(1, 2, 2, 3, pi, 10, 0, 1), 4))
-	 expect_equal(sortrows(mx, 2), matrix(c(2, 3, 1, 2, 0, 1, pi, 10), 4))
+	expect_equal(sortrows(mx, 2), matrix(c(2, 3, 1, 2, 0, 1, pi, 10), 4))
-	 expect_equal(sortrows(mx, 1:2), mx[order(mx[, 1], mx[, 2]), ])
+	expect_equal(sortrows(mx, 1:2), mx[order(mx[, 1], mx[, 2]), ])
 })
 
+# FIXME: failing tests
 test_that("cell works as expected", {
 	expect_equal(cell(0), array(dim = c(0, 0)))
 	expect_equal(cell(1), array(dim = c(1, 1)))
@@ -217,4 +218,28 @@ test_that("nargin works correctly", {
 	expect_equal(addme(13, 42), 55)
 	expect_equal(addme(13), 26)
 	expect_equal(addme(), 0)
+})
+
+test_that("setdiff works as expected", {
+	A <- c(3, 6, 2, 1, 5, 1, 1)
+	B <- c(2, 4, 6)
+	C <- c(1, 3, 5)
+	expect_equal(setdiff(A, B), C)
+	A <- data.frame(
+		Var1 = 1:5,
+		Var2 = LETTERS[1:5],
+		Var3 = c(FALSE, TRUE, FALSE, TRUE, FALSE)
+	)
+	B <- data.frame(
+		Var1 = seq(1, 9, by = 2),
+		Var2 = LETTERS[seq(1, 9, by = 2)],
+		Var3 = rep(FALSE, 5)
+	)
+	C <- data.frame(
+		Var1 = c(2, 4),
+		Var2 = c('B', 'D'),
+		Var3 = c(TRUE, TRUE)
+	)
+	expect_equal(setdiff(A, B), C)
+	# TODO: add more examples from https://se.mathworks.com/help/matlab/ref/double.setdiff.html;jsessionid=0d8d42582d4d299b8224403899f1
 })