Several fixes for cleaner check

R/greedyMix.R

@@ -294,14 +294,15 @@ greedyMix <- function(
 	data <- data[, seq_len(ncol(data) - 1)]
 
 	# ASK: remove?
-	# h0 = findobj('Tag','filename1_text');  inp = get(h0,'String');
-	# h0 = findobj('Tag','filename2_text');
+	# h0 = findobj('Tag','filename1_text')
+	# inp = get(h0,'String');
+	# h0 = findobj('Tag','filename2_text')
 	# outp = get(h0,'String');
 
-	# changesInLogml <- writeMixtureInfo(
-	# 	logml, rowsFromInd, data, adjprior, priorTerm, outp, inp,
-	# 	popnames, fixedK
-	# ) # TODO translate
+	changesInLogml <- writeMixtureInfo(
+		logml, rowsFromInd, data, adjprior, priorTerm, outp, inp,
+		popnames, fixedK
+	) # FIXMEL depends on get function above
 
 	# viewMixPartition(PARTITION, popnames) # ASK translate? On graph folder
 

R/handleData.R

@@ -53,12 +53,12 @@ handleData <- function(raw_data) {
 		)
 	}
 
-	nind <- max(data[, end])
+	nind <- max(data[, ncol(data)])
 	nrows <- size(data, 1)
 	ncols <- size(data, 2)
 	rowsFromInd <- zeros(nind, 1)
 	for (i in 1:nind) {
-		rowsFromInd[i] <- length(find(data[, end] == i))
+		rowsFromInd[i] <- length(find(data[, ncol(data)] == i))
 	}
 	maxRowsFromInd <- max(rowsFromInd)
 	a <- -999
@@ -81,7 +81,7 @@ handleData <- function(raw_data) {
 			repmat(1 / noalle[j], c(noalle[j], 1)),
 			ones(max(noalle) - noalle[j], 1)
 		))
-		priorTerm <- priorTerm + noalle[j] * gammaln(1 / noalle[j])
+		priorTerm <- priorTerm + noalle[j] * lgamma(1 / noalle[j])
 	}
 	out <- list(
 		newData = newData,

R/linkage.R

@@ -7,7 +7,7 @@
 #' @param Y data
 #' @param method either 'si', 'av', 'co' 'ce' or 'wa'
 #' @export
-linkage <- function(Y, method) {
+linkage <- function(Y, method = 'co') {
 	k <- size(Y)[1]
 	n <- size(Y)[2]
 	m <- (1 + sqrt(1 + 8 * n)) / 2
@@ -17,10 +17,7 @@ linkage <- function(Y, method) {
 			'of the PDIST function in size.'
 		)
 	}
-	if (nargin == 1) { # set default switch to be 'co'
-		method <- 'co'
-	}
-	method <- lower(method[1:2]) # simplify the switch string.
+	method <- tolower(substr(method, 1, 2)) # simplify the switch string.
 	monotonic <- 1
 	Z <- zeros(m - 1, 3) # allocate the output matrix.
 	N <- zeros(1, 2 * m - 1)

R/writeMixtureInfo.R

@@ -14,7 +14,6 @@
 #' @param COUNTS COUNTS
 #' @param SUMCOUNTS SUMCOUNTS
 #' @param LOGDIFF LOGDIFF
-#' @return changesInLogml
 #' @export
 writeMixtureInfo <- function(
 	logml, rowsFromInd, data, adjprior, priorTerm, outPutFile, inputFile, partitionSummary, popnames, fixedK, PARTITION, COUNTS, SUMCOUNTS,
@@ -100,7 +99,7 @@ writeMixtureInfo <- function(
 		while (length(text) > 58) {
 			# Take one line and display it.
 			new_line <- takeLine(text, 58)
-			text <- (length(new_line) + 1):end
+			text <- (length(new_line) + 1):length(text)
 			cat(new_line)
 			if (fid != -1) {
 				append(fid, new_line)
@@ -228,7 +227,7 @@ writeMixtureInfo <- function(
 					sum(dist2 * log2((dist2 + 10 ^ -10) / (dist1 + 10 ^ -10)))
 				) / nloci
 				div <- (div12 + div21) / 2
-				dist_mat(pop1, pop2) <- div
+				dist_mat[pop1, pop2] <- div
 			}
 		}
 

man/linkage.Rd

@@ -4,7 +4,7 @@
 \alias{linkage}
 \title{Linkage}
 \usage{
-linkage(Y, method)
+linkage(Y, method = "co")
 }
 \arguments{
 \item{Y}{data}

man/writeMixtureInfo.Rd

@@ -50,9 +50,6 @@ writeMixtureInfo(
 
 \item{LOGDIFF}{LOGDIFF}
 }
-\value{
-changesInLogml
-}
 \description{
 Writes information about the mixture
 }