Updated documentation

NAMESPACE

@@ -10,6 +10,8 @@ export(computeIndLogml)
 export(computePersonalAllFreqs)
 export(computeRows)
 export(etsiParas)
+export(fgetl)
+export(fopen)
 export(greedyMix)
 export(handleData)
 export(initPopNames)
@@ -21,6 +23,7 @@ export(linkage)
 export(logml2String)
 export(lueGenePopData)
 export(lueNimi)
+export(min_MATLAB)
 export(noIndex)
 export(ownNum2Str)
 export(poistaLiianPienet)

R/greedyMix.R

@@ -156,8 +156,7 @@ greedyMix <- function(
 # 			h0 = findobj('Tag','filename1_text');
 # 			set(h0,'String',filename); clear h0;
 
-			browser()#TEMP
+			list_dranap <- handleData(data)
-			list_dranap <- handleData(data) # FIXME: debug
 			data        <- list_dranap$newData
 			rowsFromInd <- list_dranap$rowsFromInd
 			alleleCodes <- list_dranap$alleleCodes
@@ -253,7 +252,7 @@ greedyMix <- function(
 	POP_LOGML       <- vector()
 	clearGlobalVars <- vector()
 	# ==========================================================================
-
+	c             <- list()
 	c$data        <- data
 	c$noalle      <- noalle
 	c$adjprior    <- adjprior
@@ -267,34 +266,34 @@ greedyMix <- function(
 	c$rows <- c(ekat, ekat + rowsFromInd - 1)
 
 	# partition compare
-	if (!is.null(partitionCompare)) {
+	# if (!is.null(partitionCompare)) {
-		nsamplingunits <- size(c$rows, 1)
+	# 	nsamplingunits <- size(c$rows, 1)
-		partitions     <- partitionCompare$partitions
+	# 	partitions     <- partitionCompare$partitions
-		npartitions    <- size(partitions, 2)
+	# 	npartitions    <- size(partitions, 2)
-		partitionLogml <- zeros(1, npartitions)
+	# 	partitionLogml <- zeros(1, npartitions)
-		for (i in seq_len(npartitions)) {
+	# 	for (i in seq_len(npartitions)) {
-			# number of unique partition lables
+	# 		# number of unique partition lables
-			npops <- length(unique(partitions[, i]))
+	# 		npops <- length(unique(partitions[, i]))
 
-			partitionInd <- zeros(ninds * rowsFromInd, 1)
+	# 		partitionInd <- zeros(ninds * rowsFromInd, 1)
-			partitionSample <- partitions[, i]
+	# 		partitionSample <- partitions[, i]
-			for (j in seq_len(nsamplingunits)) {
+	# 		for (j in seq_len(nsamplingunits)) {
-				partitionInd[c$rows[j, 1]:c$rows[j, 2]] <- partitionSample[j]
+	# 			partitionInd[c$rows[j, 1]:c$rows[j, 2]] <- partitionSample[j]
-			}
+	# 		}
-			# partitionLogml[i] = initialCounts(
+	# 		# partitionLogml[i] = initialCounts(
-			# 	partitionInd,
+	# 		# 	partitionInd,
-			# 	data[, seq_len(end - 1)],
+	# 		# 	data[, seq_len(end - 1)],
-			# 	npops,
+	# 		# 	npops,
-			# 	c$rows,
+	# 		# 	c$rows,
-			# 	noalle,
+	# 		# 	noalle,
-			# 	adjprior
+	# 		# 	adjprior
-			# ) #TODO translate
+	# 		# ) #TODO translate
-		}
+	# 	}
-		# return the logml result
+	# 	# return the logml result
-		partitionCompare$logmls <- partitionLogml
+	# 	partitionCompare$logmls <- partitionLogml
-		# set(h1, 'userdata', partitionCompare) # ASK remove?
+	# 	# set(h1, 'userdata', partitionCompare) # ASK remove?
-		return()
+	# 	return()
-	}
+	# }
 
 	# ASK remove (graphical part)?
 	# if (fixedK) {
@@ -312,10 +311,11 @@ greedyMix <- function(
 	# h0 = findobj('Tag','filename2_text')
 	# outp = get(h0,'String');
 
+	browser() # TEMP
 	changesInLogml <- writeMixtureInfo(
 		logml, rowsFromInd, data, adjprior, priorTerm, outp, inp,
 		popnames, fixedK
-	) # FIXMEL depends on get function above
+	) # FIXME: broken
 
 	# viewMixPartition(PARTITION, popnames) # ASK translate? On graph folder
 

man/fgetl.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fgetl.R
+% Please edit documentation in R/fgetl-fopen.R
 \name{fgetl}
 \alias{fgetl}
 \title{Read line from file, removing newline characters}

man/fopen.Rd

@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/fgetl.R
+% Please edit documentation in R/fgetl-fopen.R
 \name{fopen}
 \alias{fopen}
 \title{Open file}

man/linkage.Rd

@@ -7,7 +7,7 @@
 linkage(Y, method = "co")
 }
 \arguments{
-\item{Y}{data}
+\item{Y}{matrix}
 
 \item{method}{either 'si', 'av', 'co' 'ce' or 'wa'}
 }
@@ -19,4 +19,9 @@ Z = LINKAGE(Y) creates a hierarchical cluster tree, using the single
 linkage algorithm.  The input Y is a distance matrix such as is generated by
 PDIST. Y may also be a more general dissimilarity matrix conforming to the
 output format of PDIST.
+
+Z = linkage(X) returns a matrix Z that encodes a tree containing hierarchical clusters of the rows of the input data matrix X.
+}
+\note{
+This is also a base Matlab function. The reason why the source code is also present here is unclear.
 }

man/lueNimi.Rd

@@ -13,5 +13,5 @@ lueNimi(line)
 nimi
 }
 \description{
-Reads the line name
+Returns the part of the line from the beginning that is before the comma. Useful for returning the name of a GenePop area
 }

man/min_MATLAB.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/min.R
+\name{min_MATLAB}
+\alias{min_MATLAB}
+\title{Minimum (MATLAB version)}
+\usage{
+min_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/rivinSisaltamienMjonojenLkm.Rd

@@ -13,5 +13,5 @@ rivinSisaltamienMjonojenLkm(line)
 count
 }
 \description{
-Number of M queues
+Returns the number of queues contained in the line. There must be a space between the queues.
 }

man/testaaGenePopData.Rd

@@ -9,6 +9,12 @@ testaaGenePopData(tiedostonNimi)
 \arguments{
 \item{tiedostonNimi}{Filename}
 }
+\value{
+kunnossa (binary "ok" condition value) == 0 if the data is not valid genePop data. Otherwise, kunnossa == 1.
+}
 \description{
 Tests GenePop data
 }
+\details{
+GenePop data are textfiles that follow the GenePop format. This function checks if such file is properly formatted as GenePop.
+}

man/testaaPop.Rd

@@ -10,7 +10,7 @@ testaaPop(rivi)
 \item{rivi}{Line}
 }
 \value{
-pal
+pal = 1 if the line starts with one of the following
 }
 \description{
 Test a line in the population