Merge branch 'baps-file' into issue-2-greedy-test

R/greedyMix.R

@@ -68,19 +68,19 @@ greedyMix <- function(
 			# 	fprintf(1,'Data: %s\n',[pathname filename]);
 			# end
 
-			data <- read.delim(pathname_filename) # TODO: discover delimiter
+			data <- read.delim(pathname_filename, header = FALSE, sep = " ")
 			ninds <- testaaOnkoKunnollinenBapsData(data)  # testing
 			if (ninds == 0) stop('Incorrect Data-file')
 
 			# ASK: remove?
 			# h0 = findobj('Tag','filename1_text');
 			# set(h0,'String',filename); clear h0;
-			cat(
+			message(
 				'When using data which are in BAPS-format,',
 				'you can specify the sampling populations of the',
 				'individuals by giving two additional files:',
 				'one containing the names of the populations,',
-				'the other containing the indices of the first',
+				'the other containing the indices of the first ',
 				'individuals of the populations.'
 			)
 			input_pops <- inputdlg(

R/testaaOnkoKunnollinenBapsData.R

@@ -7,13 +7,13 @@ testaaOnkoKunnollinenBapsData <- function(data) {
 	# Tarkastaa onko viimeisess?sarakkeessa kaikki
 	# luvut 1,2,...,n johonkin n:<3A><>n asti.
 	# Tarkastaa lis<69>ksi, ett?on v<>hint<6E><74>n 2 saraketta.
-	if (size[data, 1] < 2) {
+	if (size(data, 1) < 2) {
 		ninds <- 0
 		return(ninds)
 	}
 	lastCol <- data[, ncol(data)]
 	ninds <- max(lastCol)
-	if (t(1:ninds) != unique(lastCol)) {
+	if (any(1:ninds != unique(lastCol))) {
 		ninds <- 0
 		return(ninds)
 	}

tests/testthat/test-greedyMix.R

@@ -2,8 +2,8 @@ context("Opening files on greedyMix")
 
 # TODO: needs #12 to be fixed before this can be done without user intervention
 greedyMix(
-	tietue = "inst/ext/ExamplesDataFormatting/Example baseline data in GENEPOP format for Trained clustering.txt",
-	format = "GenePop",
+	tietue = "inst/ext/ExamplesDataFormatting/Example data in BAPS format for clustering of diploid individuals.txt",
+	format = "BAPS",
 	savePreProcessed = FALSE
 ) # Upper bounds 100 100