Merge branch 'translate-admixture_initialization' into translate-indMix

R/admixture_initialization.R

@@ -0,0 +1,17 @@
+#'@title Seuraavat kolme funktiota liittyvat alkupartition muodostamiseen.
+
+admixture_initialization <- function (data_matrix, nclusters, Z) {
+	size_data <- size(data_matrix)
+	nloci <- size_data[2] - 1
+	n <- max(data_matrix[, end])
+	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)
+		for (j in 1:length(here)) {
+			initial_partition[here[j], 1] <- kori
+		}
+	}
+	return(initial_partition)
+}

R/clearGlobalVars.R

@@ -1,5 +1,5 @@
 clearGlobalVars <- function() {
-	COUNTS <- SUMCOUNTS <- PARTITION <- POP_LOGML <- vector() # placeholders
+	# COUNTS <- SUMCOUNTS <- PARTITION <- POP_LOGML <- vector() # placeholders
 	COUNTS <<- vector()
 	SUMCOUNTS <<- vector()
 	PARTITION <<- vector()

R/greedyMix.R

@@ -11,10 +11,11 @@ greedyMix <- function(
 	savePreProcessed = NULL,
 	filePreProcessed = NULL
 ) {
-	# ASK: graphical components. Remove?
+	# ASK: Unclear when fixedk == TRUE. Remove?
 	# check whether fixed k mode is selected
 	# h0 <- findobj('Tag','fixk_menu')
 	# fixedK = get(h0, 'userdata');
+	fixedK <- FALSE
 
 	# if fixedK
 	# 	if ~(fixKWarning == 1) % call function fixKWarning
@@ -22,9 +23,11 @@ greedyMix <- function(
 	# 	end
 	# end
 
+	# ASK: ditto
 	# % check whether partition compare mode is selected
 	# h1 = findobj('Tag','partitioncompare_menu');
 	# partitionCompare = get(h1, 'userdata');
+	partitionCompare <- FALSE
 
 	if (is(tietue, "list") | is(tietue, "character")) {
 		# ----------------------------------------------------------------------
@@ -244,13 +247,15 @@ greedyMix <- function(
 	}
 
 	# ==========================================================================
-	# Declaring global variables
+	# Declaring global variables and changing environment of children functions
 	# ==========================================================================
 	PARTITION       <- vector()
 	COUNTS          <- vector()
 	SUMCOUNTS       <- vector()
 	POP_LOGML       <- vector()
-	clearGlobalVars <- vector()
+	clearGlobalVars()
+
+	environment(writeMixtureInfo) <- environment()
 	# ==========================================================================
 	c             <- list()
 	c$data        <- data
@@ -265,6 +270,7 @@ greedyMix <- function(
 	ekat   <- t(seq(1, ninds, rowsFromInd) * rowsFromInd)
 	c$rows <- c(ekat, ekat + rowsFromInd - 1)
 
+	# ASK remove?
 	# partition compare
 	# if (!is.null(partitionCompare)) {
 	# 	nsamplingunits <- size(c$rows, 1)
@@ -291,17 +297,22 @@ greedyMix <- function(
 	# 	}
 	# 	# return the logml result
 	# 	partitionCompare$logmls <- partitionLogml
-	# 	# set(h1, 'userdata', partitionCompare) # ASK remove?
+	# 	# set(h1, 'userdata', partitionCompare)
 	# 	return()
 	# }
 
-	# ASK remove (graphical part)?
-	# if (fixedK) {
-	# 	#logml_npops_partitionSummary <- indMix_fixK(c) # ASK translate?
-	# } else {
-	# 	#logml_npops_partitionSummary <- indMix(c) # ASK translate?
-	# }
-	# if (logml_npops_partitionSummary$logml == 1) return()
+	if (fixedK) {
+		# logml_npops_partitionSummary <- indMix_fixK(c) # TODO: translate
+		# logml <- logml_npops_partitionSummary$logml
+		# npops <- logml_npops_partitionSummary$npops
+		# partitionSummary <- logml_npops_partitionSummary$partitionSummary
+	} else {
+		logml_npops_partitionSummary <- indMix(c) # TODO: translate
+		logml <- logml_npops_partitionSummary$logml
+		npops <- logml_npops_partitionSummary$npops
+		partitionSummary <- logml_npops_partitionSummary$partitionSummary
+	}
+	if (logml_npops_partitionSummary$logml == 1) return()
 
 	data <- data[, seq_len(ncol(data) - 1)]
 
@@ -310,8 +321,9 @@ greedyMix <- function(
 	# inp = get(h0,'String');
 	# h0 = findobj('Tag','filename2_text')
 	# outp = get(h0,'String');
+	inp <- vector()
+	outp <- vector()
 
-	browser() # TEMP
 	changesInLogml <- writeMixtureInfo(
 		logml, rowsFromInd, data, adjprior, priorTerm, outp, inp,
 		popnames, fixedK

R/indMix.R

@@ -1157,22 +1157,6 @@ indMix <- function(c, npops, dispText) {
 
 
 # %--------------------------------------------------------------------------
-# %Seuraavat kolme funktiota liittyvat alkupartition muodostamiseen.
-
-# function initial_partition=admixture_initialization(data_matrix,nclusters, Z)
-
-# size_data=size(data_matrix);
-# nloci=size_data(2)-1;
-# n=max(data_matrix(:,end));
-# T=cluster_own(Z,nclusters);
-# initial_partition=zeros(size_data(1),1);
-# for i=1:n
-#     kori=T(i);
-#     here=find(data_matrix(:,end)==i);
-#     for j=1:length(here)
-#         initial_partition(here(j),1)=kori;
-#     end
-# end
 
 # function T = cluster_own(Z,nclust)
 # true=logical(1);

R/min_MATLAB.R

@@ -30,4 +30,6 @@ min_MATLAB <- function(X, indices = TRUE) {
 	} else {
 		return(mins)
 	}
-}
+}
+
+# TODO: consider using methods instead (maybe for the package)

R/writeMixtureInfo.R

@@ -10,16 +10,10 @@
 #' @param partitionSummary partitionSummary
 #' @param popnames popnames
 #' @param fixedK fixedK
-#' @param PARTITION PARTITION
-#' @param COUNTS COUNTS
-#' @param SUMCOUNTS SUMCOUNTS
-#' @param LOGDIFF LOGDIFF
 #' @export
 writeMixtureInfo <- function(
-	logml, rowsFromInd, data, adjprior, priorTerm, outPutFile, inputFile, partitionSummary, popnames, fixedK, PARTITION, COUNTS, SUMCOUNTS,
-	LOGDIFF
+	logml, rowsFromInd, data, adjprior, priorTerm, outPutFile, inputFile, partitionSummary, popnames, fixedK
 ) {
-
 	changesInLogml <- list()
 	ninds <- size(data, 1) / rowsFromInd
 	npops <- size(COUNTS, 3)
@@ -30,7 +24,6 @@ writeMixtureInfo <- function(
 		fid <- load(outPutFile)
 	} else {
 		fid <- -1
-		message('Diverting output to baps4_output.baps')
 		# TODO: replace sink with option that will record input and output
 		sink('baps4_output.baps', split=TRUE) # save in text anyway.
 	}

man/min_MATLAB.Rd

@@ -1,9 +1,11 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/min.R
+% Please edit documentation in R/min.R, R/min_MATLAB.R
 \name{min_MATLAB}
 \alias{min_MATLAB}
 \title{Minimum (MATLAB version)}
 \usage{
+min_MATLAB(X, indices = TRUE)
+
 min_MATLAB(X, indices = TRUE)
 }
 \arguments{
@@ -12,11 +14,17 @@ min_MATLAB(X, indices = TRUE)
 \item{indices}{return indices?}
 }
 \value{
+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
 }
 \author{
+Waldir Leoncio
+
 Waldir Leoncio
 }

man/writeMixtureInfo.Rd

@@ -14,11 +14,7 @@ writeMixtureInfo(
   inputFile,
   partitionSummary,
   popnames,
-  fixedK,
-  PARTITION,
-  COUNTS,
-  SUMCOUNTS,
-  LOGDIFF
+  fixedK
 )
 }
 \arguments{
@@ -41,14 +37,6 @@ writeMixtureInfo(
 \item{popnames}{popnames}
 
 \item{fixedK}{fixedK}
-
-\item{PARTITION}{PARTITION}
-
-\item{COUNTS}{COUNTS}
-
-\item{SUMCOUNTS}{SUMCOUNTS}
-
-\item{LOGDIFF}{LOGDIFF}
 }
 \description{
 Writes information about the mixture

tests/testthat/test-greedyMix.R

@@ -1,11 +1,7 @@
-# library(devtools)#TEMP
-library(testthat)#TEMP
-# library(rBAPS)#TEMP
-
 context("Opening files on greedyMix")
 
 greedyMix(
-	tietue = "data/ExamplesDataFormatting/Example baseline data in GENEPOP format for Trained clustering.txt",
+	tietue = "inst/ext/ExamplesDataFormatting/Example baseline data in GENEPOP format for Trained clustering.txt",
 	format = "GenePop",
 	savePreProcessed = FALSE
 )