Merge branch 'clean-check' into import-genepop

.Rbuildignore

@@ -1,6 +1,6 @@
 LICENSE
 TODO.md
-matlab
+^matlab
 CHANGELOG.md
 CITATION.cff
 .travis.yml

NAMESPACE

@@ -23,6 +23,7 @@ export(linkage)
 export(logml2String)
 export(lueGenePopData)
 export(lueNimi)
+export(matlab2r)
 export(noIndex)
 export(ownNum2Str)
 export(poistaLiianPienet)
@@ -49,3 +50,4 @@ export(writeMixtureInfo)
 importFrom(methods,is)
 importFrom(stats,runif)
 importFrom(utils,read.delim)
+importFrom(utils,write.table)

R/admixture_initialization.R

@@ -6,12 +6,12 @@
 admixture_initialization <- function (data_matrix, nclusters, Z) {
 	size_data <- size(data_matrix)
 	nloci <- size_data[2] - 1
-	n <- max(data_matrix[, end])
+	n <- max(data_matrix[, ncol(data_matrix)])
 	T <- cluster_own(Z, nclusters)
 	initial_partition <- zeros(size_data[1], 1)
 	for (i in 1:n) {
 		kori <- T[i]
-		here <- find(data_matrix[,end] == i)
+		here <- find(data_matrix[, ncol(data_matrix)] == i)
 		for (j in 1:length(here)) {
 			initial_partition[here[j], 1] <- kori
 		}

R/clearGlobalVars.R

@@ -1,8 +1,7 @@
 clearGlobalVars <- function() {
-	# COUNTS <- SUMCOUNTS <- PARTITION <- POP_LOGML <- vector() # placeholders
+	COUNTS <- vector()
-	COUNTS <<- vector()
+	SUMCOUNTS <- vector()
-	SUMCOUNTS <<- vector()
+	PARTITION <- vector()
-	PARTITION <<- vector()
+	POP_LOGML <- vector()
-	POP_LOGML <<- vector()
+	LOGDIFF <- vector()
-	LOGDIFF <<- vector()
 }

R/cluster_own.R

@@ -15,7 +15,7 @@ cluster_own <- function(Z, nclust) {
 		for (k in (m - maxclust + 1):(m - 1)) {
 			i = Z(k, 1) # left tree
 			if (i <= m) { # original node, no leafs
-				T(i) = clsnum
+				T[i] = clsnum
 				clsnum = clsnum + 1
 			} else if (i < (2 * m - maxclust + 1)) { # created before cutoff, search down the tree
 				T <- clusternum(Z, T, i - m, clsnum)

R/computeDiffInCounts.R

@@ -9,8 +9,8 @@ computeDiffInCounts <- function(rows, max_noalle, nloci, data) {
 		notEmpty <- find(row>=0)
 
 		if (length(notEmpty) > 0) {
-			diffInCounts(row(notEmpty) + (notEmpty - 1) * max_noalle) <-
+			diffInCounts[row(notEmpty) + (notEmpty - 1) * max_noalle] <-
-				diffInCounts(row(notEmpty) + (notEmpty - 1) * max_noalle) + 1
+				diffInCounts[row(notEmpty) + (notEmpty - 1) * max_noalle] + 1
 		}
 	}
 	return(diffInCounts)

R/globals.R

@@ -0,0 +1 @@
+utils::globalVariables(c("PARTITION", "COUNTS", "SUMCOUNTS", "LOGDIFF", "POP_LOGML"))

R/indMix.R

@@ -52,7 +52,7 @@ indMix <- function(c, npops, dispText) {
 		} else {
 			npopsTaulu <- as.numeric(npopstext)
 			ykkoset <- find(npopsTaulu == 1)
-			npopsTaulu(ykkoset) <- list() # Mik<69>li ykk<6B>si<73> annettu yl<79>rajaksi, ne poistetaan.
+			npopsTaulu[ykkoset] <- list() # Mik<69>li ykk<6B>si<73> annettu yl<79>rajaksi, ne poistetaan.
 			if (isempty(npopsTaulu)) {
 				logml <- 1
 				partitionSummary <- 1
@@ -68,7 +68,7 @@ indMix <- function(c, npops, dispText) {
 	nruns <- length(npopsTaulu)
 
 	initData <- data
-	data <- data[,1:(end - 1)]
+	data <- data[,1:(ncol(data) - 1)]
 
 	logmlBest <- -1e50
 	partitionSummary <- -1e50 * ones(30, 2) # Tiedot 30 parhaasta partitiosta (npops ja logml)
@@ -76,13 +76,13 @@ indMix <- function(c, npops, dispText) {
 	worstLogml <- -1e50
 	worstIndex <- 1
 	for (run in 1:nruns) {
-		npops <- npopsTaulu(run)
+		npops <- npopsTaulu[run]
 		if (dispText) {
 			dispLine()
 			print(
 				paste0(
-					'Run ', num2str(run), '/', num2str(nruns),
+					'Run ', as.character(run), '/', as.character(nruns),
-					', maximum number of populations ', num2str(npops), '.'
+					', maximum number of populations ', as.character(npops), '.'
 				)
 			)
 		}
@@ -120,7 +120,7 @@ indMix <- function(c, npops, dispText) {
 			print(
 				paste0(
 					'Mixture analysis started with initial',
-					num2str(npops),
+					as.character(npops),
 					'populations.'
 				)
 			)
@@ -130,7 +130,7 @@ indMix <- function(c, npops, dispText) {
 			muutoksia <- 0
 
 			if (dispText) {
-				print(paste('Performing steps:', num2str(roundTypes)))
+				print(paste('Performing steps:', as.character(roundTypes)))
 			}
 
 			for (n in 1:length(roundTypes)) {
@@ -545,7 +545,7 @@ indMix <- function(c, npops, dispText) {
 		npops <- poistaTyhjatPopulaatiot(npops)
 		POP_LOGML <- computePopulationLogml(1:npops, adjprior, priorTerm)
 		if (dispText) {
-			print(paste('Found partition with', num2str(npops), 'populations.'))
+			print(paste('Found partition with', as.character(npops), 'populations.'))
 			print(paste('Log(ml) =', as.character(logml)))
 			print(' ')
 		}

R/initialPopCounts.R

@@ -7,11 +7,11 @@ initialPopCounts <- function(data, npops, rows, noalle, adjprior) {
 		for (j in 1:nloci) {
 			i_rivit <- rows(i, 1):rows(i, 2)
 			havainnotLokuksessa <- find(data[i_rivit, j] >= 0)
-			sumcounts(i, j) <- length(havainnotLokuksessa)
+			sumcounts[i, j] <- length(havainnotLokuksessa)
 			for (k in 1:noalle[j]) {
 				alleleCode <- k
 				N_ijk <- length(find(data[i_rivit, j] == alleleCode))
-				counts(k, j, i) <- N_ijk
+				counts[k, j, i] <- N_ijk
 			}
 		}
 	}

R/laskeLoggis.R

@@ -1,7 +1,7 @@
 laskeLoggis <- function(counts, sumcounts, adjprior) {
 	npops <- size(counts, 3)
 
-	sum1 <- sum(sum(sum(gammaln(counts + repmat(adjprior, c(1, 1, npops))))))
+	sum1 <- sum(sum(sum(lgamma(counts + repmat(adjprior, c(1, 1, npops))))))
 	sum3 <- sum(sum(lgamma(adjprior))) - sum(sum(lgamma(1 + sumcounts)))
 	logml2 <- sum1 - npops * sum3
 	loggis <- logml2

R/laskeOsaDist.R

@@ -1,9 +1,15 @@
+#' @title Lower part of the dist
+#' @description Constructs from the dist vector a subvector containing the individual inds2, Forms dist sub-vectors the vector, which includes yksiliden inds2
+#' @param inds2 inds2
+#' @param dist dist
+#' @param ninds ninds
+#' @author Waldir Leoncio
 laskeOsaDist <- function(inds2, dist, ninds) {
 	# % Muodostaa dist vektorista osavektorin, joka sis<69>lt<6C><74> yksil<69>iden inds2
 	# % v<>liset et<65>isyydet. ninds=kaikkien yksil<69>iden lukum<75><6D>r<EFBFBD>.
 
 	ninds2 <- length(inds2)
-	apu <- zeros(nchoosek(ninds2, 2), 2)
+	apu <- zeros(choose(ninds2, 2), 2)
 	rivi <- 1
 	for (i in 1:ninds2-1) {
 		for (j in i+1:ninds2) {

R/matlab2r.R

@@ -4,6 +4,7 @@
 #' @param saveOutput if `TRUE`, `filename` is overwritten. Defaults to `FALSE`
 #' @return text converted to R, printed to screen or replacing input file
 #' @author Waldir Leoncio
+#' @importFrom utils write.table
 #' @export
 matlab2r <- function(filename, saveOutput = FALSE) {
 	# Verification
@@ -21,7 +22,7 @@ matlab2r <- function(filename, saveOutput = FALSE) {
 	txt <- gsub("for (.+)=(.+)", "for (\\1 in \\2) {", txt)
 	txt <- gsub("end", "}", txt)
 	txt <- gsub("(.),(\\S)", "\\1, \\2", txt)
-	# TODO: replace forms like (:,:) with [, ]
+	# TODO: replace forms like (:,:) with [, ] if they come before <-
 	# TODO: add argument to skip some of these rules
 	txt <- gsub("if (.+)", "if (\\1) {", txt) # FIXME: paste comments after {
 	txt <- gsub("else$", "} else {", txt)

R/poistaLiianPienet.R

@@ -41,7 +41,7 @@ poistaLiianPienet <- function (npops, rowsFromInd, alaraja,
         PARTITION[yksilot] == n
     }
 
-    # TODO: add COUNTS, SUMCOUNTS and PARTITION to return or use <<-
+    # TODO: add COUNTS, SUMCOUNTS and PARTITION to return or use <-
     COUNTS[, , miniPops] <- NA
     SUMCOUNTS[miniPops, ] <- NA
 

R/poistaTyhjatPopulaatiot.R

@@ -2,13 +2,13 @@ poistaTyhjatPopulaatiot <- function(npops) {
 	# % Poistaa tyhjentyneet populaatiot COUNTS:ista ja
 	# % SUMCOUNTS:ista. P<>ivitt<74><74> npops:in ja PARTITION:in.
 	notEmpty <- find(any(SUMCOUNTS, 2))
-	COUNTS <<- COUNTS[, , notEmpty]
+	COUNTS <- COUNTS[, , notEmpty]
-	SUMCOUNTS <<- SUMCOUNTS[notEmpty, ]
+	SUMCOUNTS <- SUMCOUNTS[notEmpty, ]
-	LOGDIFF <<- LOGDIFF[, notEmpty]
+	LOGDIFF <- LOGDIFF[, notEmpty]
 
 	for (n in 1:length(notEmpty)) {
 		apu <- find(PARTITION == notEmpty(n))
-		PARTITION(apu) <<- n
+		PARTITION[apu] <- n
 	}
 	npops <- length(notEmpty)
 	return(npops)

R/updateGlobalVariables.R

@@ -2,21 +2,21 @@ updateGlobalVariables <- function(ind, i2, diffInCounts, adjprior, priorTerm) {
 	# % Suorittaa globaalien muuttujien muutokset, kun yksil<69> ind
 	# % on siirret<65><74>n koriin i2.
 
-	i1 <- PARTITION(ind)
+	i1 <- PARTITION[ind]
-	PARTITION(ind) <<- i2
+	PARTITION[ind] <- i2
 
-	COUNTS[, , i1] <<- COUNTS[, , i1] - diffInCounts
+	COUNTS[, , i1] <- COUNTS[, , i1] - diffInCounts
-	COUNTS[, , i2] <<- COUNTS[, , i2] + diffInCounts
+	COUNTS[, , i2] <- COUNTS[, , i2] + diffInCounts
-	SUMCOUNTS[i1, ] <<- SUMCOUNTS[i1, ] - sum[diffInCounts]
+	SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - sum[diffInCounts]
-	SUMCOUNTS[i2, ] <<- SUMCOUNTS[i2, ] + sum[diffInCounts]
+	SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + sum[diffInCounts]
 
-	POP_LOGML[c(i1, i2)] <<- computePopulationLogml(
+	POP_LOGML[c(i1, i2)] <- computePopulationLogml(
 		c(i1, i2), adjprior, priorTerm
 	)
 
-	LOGDIFF[, c(i1, i2)] <<- -Inf
+	LOGDIFF[, c(i1, i2)] <- -Inf
 	inx <- c(find(PARTITION == i1), find(PARTITION==i2))
-	LOGDIFF[inx, ] <<- -Inf
+	LOGDIFF[inx, ] <- -Inf
 }
 
 updateGlobalVariables2 <- function(i1, i2, diffInCounts, adjprior, priorTerm) {
@@ -24,12 +24,12 @@ updateGlobalVariables2 <- function(i1, i2, diffInCounts, adjprior, priorTerm) {
 	# % korissa i1 olevat yksil<69>t siirret<65><74>n koriin i2.
 
 	inds <- find(PARTITION == i1)
-	PARTITION(inds) <<- i2
+	PARTITION[inds] <- i2
 
-	COUNTS[, , i1] <<- COUNTS[, , i1] - diffInCounts
+	COUNTS[, , i1] <- COUNTS[, , i1] - diffInCounts
-	COUNTS[, , i2] <<- COUNTS[, , i2] + diffInCounts
+	COUNTS[, , i2] <- COUNTS[, , i2] + diffInCounts
-	SUMCOUNTS[i1, ] <<- SUMCOUNTS[i1, ] - sum[diffInCounts]
+	SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - sum[diffInCounts]
-	SUMCOUNTS[i2, ] <<- SUMCOUNTS[i2, ] + sum[diffInCounts]
+	SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + sum[diffInCounts]
 
 	POP_LOGML[i1] <- 0
 	POP_LOGML[i2] <- computePopulationLogml(i2, adjprior, priorTerm)
@@ -47,18 +47,18 @@ updateGlobalVariables3 <- function(
 	# % koriin.
 
 	i1 <- PARTITION[muuttuvat(1)]
-	PARTITION[muuttuvat] <<- i2
+	PARTITION[muuttuvat] <- i2
 
-	COUNTS[, , i1] <<- COUNTS[, , i1] - diffInCounts
+	COUNTS[, , i1] <- COUNTS[, , i1] - diffInCounts
-	COUNTS[, , i2] <<- COUNTS[, , i2] + diffInCounts
+	COUNTS[, , i2] <- COUNTS[, , i2] + diffInCounts
-	SUMCOUNTS[i1, ] <<- SUMCOUNTS[i1, ] - sum[diffInCounts]
+	SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - sum[diffInCounts]
-	SUMCOUNTS[i2, ] <<- SUMCOUNTS[i2, ] + sum[diffInCounts]
+	SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + sum[diffInCounts]
 
-	POP_LOGML[c(i1, i2)] <<- computePopulationLogml(
+	POP_LOGML[c(i1, i2)] <- computePopulationLogml(
 		c(i1, i2), adjprior, priorTerm
 	)
 
-	LOGDIFF[, c(i1, i2)] <<- -Inf
+	LOGDIFF[, c(i1, i2)] <- -Inf
 	inx <- c(find(PARTITION == i1), find(PARTITION == i2))
-	LOGDIFF[inx, ] <<- -Inf
+	LOGDIFF[inx, ] <- -Inf
 }

man/laskeOsaDist.Rd

@@ -0,0 +1,21 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/laskeOsaDist.R
+\name{laskeOsaDist}
+\alias{laskeOsaDist}
+\title{Lower part of the dist}
+\usage{
+laskeOsaDist(inds2, dist, ninds)
+}
+\arguments{
+\item{inds2}{inds2}
+
+\item{dist}{dist}
+
+\item{ninds}{ninds}
+}
+\description{
+Constructs from the dist vector a subvector containing the individual inds2, Forms dist sub-vectors the vector, which includes yksiliden inds2
+}
+\author{
+Waldir Leoncio
+}

man/matlab2r.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/matlab2r.R
+\name{matlab2r}
+\alias{matlab2r}
+\title{Convert Matlab function to R}
+\usage{
+matlab2r(filename, saveOutput = FALSE)
+}
+\arguments{
+\item{filename}{name of the file}
+
+\item{saveOutput}{if `TRUE`, `filename` is overwritten. Defaults to `FALSE`}
+}
+\value{
+text converted to R, printed to screen or replacing input file
+}
+\description{
+Performs basic syntax conversion from Matlab to R
+}
+\author{
+Waldir Leoncio
+}