Merge work on greedyMix into develop
This commit is contained in:
Waldir Leoncio
commit
3fd1cac27b
17 changed files with 171 additions and 96 deletions
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@ -1,6 +1,6 @@
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Package: rBAPS
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Title: Bayesian Analysis of Population Structure
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Version: 0.0.0.9001
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Version: 0.0.0.9002
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Date: 2020-11-09
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Authors@R:
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c(
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7
R/cell.R
7
R/cell.R
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@ -2,9 +2,14 @@
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#' @description Creates an array of zeros
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#' @param n a the first dimension (or both, if sz is not passed)
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#' @param sz the second dimension (or 1st and 2nd, if not passed)
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#' @param expandable if TRUE, output is a list (so it can take different
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#' lengths)
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#' @param ... Other dimensions
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#' @return An array of zeroes with the dimensions passed on call
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cell <- function(n, sz = c(n, n), ...) {
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cell <- function(n, sz = c(n, n), expandable=FALSE, ...) {
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if (expandable) {
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return(vector("list", length = n))
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}
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if (length(sz) == 1 & missing(...)) {
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return(array(0, dim = c(n, sz)))
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} else if (length(sz) == 2) {
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@ -4,9 +4,9 @@ computeDiffInCounts <- function(rows, max_noalle, nloci, data) {
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# % riveill<6C> rows. rows pit<69><74> olla vaakavektori.
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diffInCounts <- zeros(max_noalle, nloci)
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for (i in rows) {
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for (i in seq_len(nrow(data)) ) {
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row <- data[i, ]
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notEmpty <- find(row>=0)
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notEmpty <- as.matrix(find(row>=0))
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if (length(notEmpty) > 0) {
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diffInCounts[row(notEmpty) + (notEmpty - 1) * max_noalle] <-
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@ -1,18 +1,26 @@
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computePopulationLogml <- function(pops, adjprior, priorTerm) {
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# Palauttaa length(pops)*1 taulukon, jossa on laskettu korikohtaiset
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# ======================================================== #
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# Limiting COUNTS size #
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# ======================================================== #
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COUNTS <- COUNTS[seq_len(nrow(adjprior)), seq_len(ncol(adjprior)), pops, drop=FALSE]
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x <- size(COUNTS, 1)
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y <- size(COUNTS, 2)
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z <- length(pops)
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popLogml <- squeeze(
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# FIXME: assumes COUNTS has 3 dims. Where does this come from?
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# ======================================================== #
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# Computation #
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# ======================================================== #
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isarray <- length(dim(repmat(adjprior, c(1, 1, length(pops))))) > 2
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term1 <- squeeze(
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sum(
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sum(
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reshape(
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lgamma(
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repmat(adjprior, c(1, 1, length(pops))) +
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COUNTS[, , pops]
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COUNTS[seq_len(nrow(adjprior)), seq_len(ncol(adjprior)), pops, drop=!isarray]
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),
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c(x, y, z)
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),
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@ -20,6 +28,8 @@ computePopulationLogml <- function(pops, adjprior, priorTerm) {
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),
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2
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)
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) - sum(lgamma(1 + SUMCOUNTS[pops, ]), 2) - priorTerm
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)
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if (is.null(priorTerm)) priorTerm <- 0
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popLogml <- term1 - sum(lgamma(1 + SUMCOUNTS[pops, ]), 2) - priorTerm
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return(popLogml)
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}
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11
R/find.R
11
R/find.R
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@ -1,10 +1,15 @@
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#' @title Find indices and values of nonzero elements
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#' @description Emulates behavior of `find`
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#' @param x object or logic operation on an object
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find <- function(x) {
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#' @param sort sort output?
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find <- function(x, sort=TRUE) {
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if (is.logical(x)) {
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return(which(x))
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out <- which(x)
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} else {
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return(which(x > 0))
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out <- which(x > 0)
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}
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if (sort) {
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out <- sort(out)
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}
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return(out)
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}
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@ -1,8 +1,8 @@
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COUNTS <- array(0, dim=c(100, 100, 100))
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SUMCOUNTS <- array(0, dim=c(100, 100))
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PARTITION <- vector()
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POP_LOGML <- vector()
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LOGDIFF <- vector()
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PARTITION <- array(1, dim=c(100))
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POP_LOGML <- array(1, dim=c(100))
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LOGDIFF <- array(1, dim=c(100, 100))
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# If handling globas break, try other ideas from https://stackoverflow.com/a/65252740/1169233
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@ -68,14 +68,15 @@ greedyMix <- function(
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# fprintf(1,'Data: %s\n',[pathname filename]);
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# end
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data <- read.delim(pathname_filename) # TODO: discover delimiter
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data <- read.delim(pathname_filename, header = FALSE, sep = " ")
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data <- as.matrix(data)
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ninds <- testaaOnkoKunnollinenBapsData(data) # testing
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if (ninds == 0) stop('Incorrect Data-file')
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# ASK: remove?
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# h0 = findobj('Tag','filename1_text');
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# set(h0,'String',filename); clear h0;
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cat(
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message(
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'When using data which are in BAPS-format,',
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'you can specify the sampling populations of the',
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'individuals by giving two additional files:',
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@ -104,8 +105,17 @@ greedyMix <- function(
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popnames <- ""
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}
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# [data, rowsFromInd, alleleCodes, noalle, adjprior, priorTerm] = handleData(data); # TODO: translate this function
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# [Z,dist] = newGetDistances(data,rowsFromInd); # TODO: translate
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temp_handleData <- handleData(data)
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data <- temp_handleData$newData
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rowsFromInd <- temp_handleData$rowsFromInd
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alleleCodes <- temp_handleData$alleleCodes
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noalle <- temp_handleData$noalle
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adjprior <- temp_handleData$adjprior
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priorTerm <- temp_handleData$priorTerm
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Z_dist <- newGetDistances(data,rowsFromInd)
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Z <- Z_dist$Z
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dist <- Z_dist$dist
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rm(temp_handleData, Z_dist)
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if (is.null(savePreProcessed)) {
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save_preproc <- questdlg(
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quest = 'Do you wish to save pre-processed data?',
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@ -307,7 +317,7 @@ greedyMix <- function(
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# npops <- logml_npops_partitionSummary$npops
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# partitionSummary <- logml_npops_partitionSummary$partitionSummary
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} else {
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logml_npops_partitionSummary <- indMix(c) # TODO: translate
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logml_npops_partitionSummary <- indMix(c)
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logml <- logml_npops_partitionSummary$logml
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npops <- logml_npops_partitionSummary$npops
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partitionSummary <- logml_npops_partitionSummary$partitionSummary
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@ -20,7 +20,7 @@ handleData <- function(raw_data) {
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# koodi pienimm?ksi koodiksi, joka isompi kuin mik??n k?yt?ss?oleva koodi.
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# T?m?n j?lkeen funktio muuttaa alleelikoodit siten, ett?yhden lokuksen j
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# koodit saavat arvoja v?lill?1,...,noalle(j).
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data <- raw_data
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data <- as.matrix(raw_data)
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nloci <- size(raw_data, 2) - 1
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dataApu <- data[, 1:nloci]
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@ -35,26 +35,31 @@ handleData <- function(raw_data) {
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# isoinAlleeli <- []
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noalle <- zeros(1, nloci)
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alleelitLokuksessa <- cell(nloci, 1)
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alleelitLokuksessa <- cell(nloci, 1, expandable=TRUE)
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for (i in 1:nloci) {
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alleelitLokuksessaI <- unique(data[, i])
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alleelitLokuksessaI_pos <- find(alleelitLokuksessaI >= 0)
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alleelitLokuksessa[i, 1] <- ifelse(
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test = length(alleelitLokuksessaI_pos) > 0,
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yes = alleelitLokuksessaI[alleelitLokuksessaI_pos],
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no = 0
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alleelitLokuksessa[[i]] <- sort(alleelitLokuksessaI[
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find(
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alleelitLokuksessaI >= 0
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)
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noalle[i] <- length(alleelitLokuksessa[i, 1])
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])
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noalle[i] <- length(alleelitLokuksessa[[i]])
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}
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alleleCodes <- zeros(max(noalle), nloci)
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for (i in 1:nloci) {
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alleelitLokuksessaI <- alleelitLokuksessa[i, 1]
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alleelitLokuksessaI <- alleelitLokuksessa[[i]]
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puuttuvia <- max(noalle) - length(alleelitLokuksessaI)
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alleleCodes[, i] <- as.matrix(
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c(alleelitLokuksessaI, zeros(puuttuvia, 1))
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)
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}
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for (loc in seq_len(nloci)) {
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for (all in seq_len(noalle[loc])) {
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data[find(data[, loc] == alleleCodes[all, loc]), loc] <- all
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}
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}
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nind <- max(data[, ncol(data)])
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nrows <- size(data, 1)
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ncols <- size(data, 2)
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90
R/indMix.R
90
R/indMix.R
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@ -21,18 +21,13 @@ indMix <- function(c, npops, dispText) {
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rm(c)
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nargin <- length(as.list(match.call())) - 1
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if (nargin < 2) {
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dispText <- 1
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npopstext <- matrix()
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ready <- FALSE
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teksti <- 'Input upper bound to the number of populations (possibly multiple values)' # TODO: add "likely ncol(Z) values"?
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while (!ready) {
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npopstextExtra <- inputdlg(
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teksti,
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1,
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'20'
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)
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npopstextExtra <- inputdlg(teksti, 1, '20')
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if (isempty(npopstextExtra)) { # Painettu Cancel:ia
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return()
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}
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@ -52,7 +47,7 @@ indMix <- function(c, npops, dispText) {
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} else {
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npopsTaulu <- as.numeric(npopstext)
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ykkoset <- find(npopsTaulu == 1)
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npopsTaulu[ykkoset] <- list() # Mik<69>li ykk<6B>si<73> annettu yl<79>rajaksi, ne poistetaan.
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npopsTaulu[ykkoset] <- NA # Mik<69>li ykk<6B>si<73> annettu yl<79>rajaksi, ne poistetaan (if ones are given as an upper limit, they are deleted)
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if (isempty(npopsTaulu)) {
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logml <- 1
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partitionSummary <- 1
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@ -79,10 +74,11 @@ indMix <- function(c, npops, dispText) {
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npops <- npopsTaulu[[run]]
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if (dispText) {
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dispLine()
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print(
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cat(
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paste0(
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'Run ', as.character(run), '/', as.character(nruns),
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', maximum number of populations ', as.character(npops), '.'
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', maximum number of populations ', as.character(npops),
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'.\n'
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)
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)
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}
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@ -115,10 +111,9 @@ indMix <- function(c, npops, dispText) {
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vaihe <- 1
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if (dispText) {
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print(' ')
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print(
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message(
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paste0(
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'Mixture analysis started with initial',
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'\nMixture analysis started with initial ',
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as.character(npops),
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' populations.'
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)
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@ -129,7 +124,7 @@ indMix <- function(c, npops, dispText) {
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muutoksia <- 0
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if (dispText) {
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print(paste('Performing steps:', as.character(roundTypes)))
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message(paste('\nPerforming steps:', as.character(roundTypes)))
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}
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for (n in 1:length(roundTypes)) {
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@ -137,26 +132,26 @@ indMix <- function(c, npops, dispText) {
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round <- roundTypes[n]
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kivaluku <- 0
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if (kokeiltu(round) == 1) { #Askelta kokeiltu viime muutoksen j<>lkeen
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if (kokeiltu[round] == 1) { #Askelta kokeiltu viime muutoksen j<>lkeen
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} else if (round == 0 | round == 1) { #Yksil<69>n siirt<72>minen toiseen populaatioon.
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inds <- 1:ninds
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aputaulu <- c(t(inds), rand(ninds, 1))
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aputaulu <- cbind(inds, rand(ninds, 1))
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aputaulu <- sortrows(aputaulu, 2)
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inds <- t(aputaulu[, 1])
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muutosNyt <- 0
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for (ind in inds) {
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i1 <- PARTITION[ind]
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muutokset_diffInCounts = laskeMuutokset(
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muutokset_diffInCounts <- laskeMuutokset(
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ind, rows, data, adjprior, priorTerm
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)
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muutokset <- muutokset_diffInCounts$muutokset
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diffInCounts <- muutokset_diffInCounts$diffInCounts
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if (round == 1) {
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maxMuutos <- max_MATLAB(muutokset)[[1]]
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i2 <- max_MATLAB(muutokset)[[2]]
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maxMuutos <- max_MATLAB(muutokset)$max
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i2 <- max_MATLAB(muutokset)$idx
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}
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if (i1 != i2 & maxMuutos > 1e-5) {
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@ -164,9 +159,7 @@ indMix <- function(c, npops, dispText) {
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muutoksia <- 1
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if (muutosNyt == 0) {
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muutosNyt <- 1
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if (dispText) {
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print('Action 1')
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}
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if (dispText) message('Action 1')
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}
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kokeiltu <- zeros(nRoundTypes, 1)
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kivaluku <- kivaluku + 1
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@ -175,14 +168,17 @@ indMix <- function(c, npops, dispText) {
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)
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logml <- logml + maxMuutos
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if (logml > worstLogml) {
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partitionSummary_added = addToSummary(
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temp_addToSum <- addToSummary(
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logml, partitionSummary, worstIndex
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)
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partitionSummary_added <- partitionSummary_added$partitionSummary
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added <- partitionSummary_added$added
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partitionSummary <- temp_addToSum$partitionSummary
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added <- temp_addToSum$added
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if (added == 1) {
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worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
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worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
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temp_minMATLAB <- min_MATLAB(
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partitionSummary[, 2]
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)
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worstLogml <- temp_minMATLAB[[1]]
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worstIndex <- temp_minMATLAB[[2]]
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}
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}
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}
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@ -191,7 +187,6 @@ indMix <- function(c, npops, dispText) {
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if (muutosNyt == 0) {
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kokeiltu[round] <- 1
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}
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} else if (round == 2) { # Populaation yhdist<73>minen toiseen.
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maxMuutos <- 0
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for (pop in 1:npops) {
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@ -218,14 +213,14 @@ indMix <- function(c, npops, dispText) {
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)
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logml <- logml + maxMuutos
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if (dispText) {
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print('Action 2')
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cat('Action 2')
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}
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if (logml > worstLogml) {
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partitionSummary_added <- addToSummary(
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temp_addToSum <- addToSummary(
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logml, partitionSummary, worstIndex
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)
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partitionSummary <- partitionSummary_added$partitionSummary
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added <- partitionSummary_added$added
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partitionSummary <- temp_addToSum$partitionSummary
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added <- temp_addToSum$added
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if (added==1) {
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worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
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worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
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@ -284,17 +279,17 @@ indMix <- function(c, npops, dispText) {
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logml <- logml + maxMuutos
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if (dispText) {
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if (round == 3) {
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print('Action 3')
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cat('Action 3')
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} else {
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print('Action 4')
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cat('Action 4')
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}
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}
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if (logml > worstLogml) {
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partitionSummary_added <- addToSummary(
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temp_addToSum <- addToSummary(
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logml, partitionSummary, worstIndex
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)
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partitionSummary <- partitionSummary_added$partitionSummary
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added <- partitionSummary_added$added
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partitionSummary <- temp_addToSum$partitionSummary
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added <- temp_addToSum$added
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if (added==1) {
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worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
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worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
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@ -365,18 +360,18 @@ indMix <- function(c, npops, dispText) {
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muutoksia <- 1 # Ulompi kirjanpito.
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if (dispText) {
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if (round == 5) {
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print('Action 5')
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cat('Action 5')
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} else {
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print('Action 6')
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cat('Action 6')
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}
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}
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}
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if (logml > worstLogml) {
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partitionSummary_added <- addToSummary(
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temp_addToSum <- addToSummary(
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logml, partitionSummary, worstIndex
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)
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partitionSummary <- partitionSummary_added$partitionSummary
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added <- partitionSummary_added$added
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partitionSummary <- temp_addToSum$partitionSummary
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added <- temp_addToSum$added
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if (added==1) {
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worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
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worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
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@ -477,11 +472,11 @@ indMix <- function(c, npops, dispText) {
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muutoksia <- 1
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logml <- logml + totalMuutos
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if (logml > worstLogml) {
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partitionSummary_added = addToSummary(
|
||||
temp_addToSum <- addToSummary(
|
||||
logml, partitionSummary, worstIndex
|
||||
)
|
||||
partitionSummary_added <- partitionSummary_added$partitionSummary
|
||||
added <- partitionSummary_added$added
|
||||
partitionSummary <- temp_addToSum$partitionSummary
|
||||
added <- temp_addToSum$added
|
||||
if (added == 1) {
|
||||
worstLogml <- min_MATLAB(partitionSummary[, 2])[[1]]
|
||||
worstIndex <- min_MATLAB(partitionSummary[, 2])[[2]]
|
||||
|
|
@ -489,7 +484,7 @@ indMix <- function(c, npops, dispText) {
|
|||
}
|
||||
if (muutoksiaNyt == 0) {
|
||||
if (dispText) {
|
||||
print('Action 7')
|
||||
cat('Action 7')
|
||||
}
|
||||
muutoksiaNyt <- 1
|
||||
}
|
||||
|
|
@ -513,7 +508,8 @@ indMix <- function(c, npops, dispText) {
|
|||
|
||||
}
|
||||
}
|
||||
|
||||
# FIXME: muutoksia is never 0, so vaihe never equals 5 and ready 1
|
||||
print(paste("i1 =", i1, "i2 =", i2, "maxMuutos =", maxMuutos))#TEMP
|
||||
if (muutoksia == 0) {
|
||||
if (vaihe <= 4) {
|
||||
vaihe <= vaihe + 1
|
||||
|
|
@ -532,7 +528,7 @@ indMix <- function(c, npops, dispText) {
|
|||
} else if (vaihe == 3) {
|
||||
roundTypes <- c(5, 5, 7)
|
||||
} else if (vaihe == 4) {
|
||||
roundTypes = c(4, 3, 1)
|
||||
roundTypes <- c(4, 3, 1)
|
||||
} else if (vaihe == 5) {
|
||||
roundTypes <- c(6, 7, 2, 3, 4, 1)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -60,7 +60,7 @@ laskeMuutokset <- function(ind, globalRows, data, adjprior, priorTerm) {
|
|||
diffInCounts <- computeDiffInCounts(
|
||||
rows, size(COUNTS, 1), size(COUNTS, 2), data
|
||||
)
|
||||
diffInSumCounts <- sum(diffInCounts)
|
||||
diffInSumCounts <- colSums(diffInCounts)
|
||||
|
||||
COUNTS[, , i1] <- COUNTS[, , i1] - diffInCounts
|
||||
SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - diffInSumCounts
|
||||
|
|
@ -68,7 +68,7 @@ laskeMuutokset <- function(ind, globalRows, data, adjprior, priorTerm) {
|
|||
COUNTS[, , i1] <- COUNTS[, , i1] + diffInCounts
|
||||
SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] + diffInSumCounts
|
||||
|
||||
i2 <- find(muutokset == -Inf) # Etsit<69><74>n populaatiot jotka muuttuneet viime kerran j<>lkeen.
|
||||
i2 <- find(muutokset == -Inf) # Etsit<69><74>n populaatiot jotka muuttuneet viime kerran j<>lkeen. (Searching for populations that have changed since the last time)
|
||||
i2 <- setdiff(i2, i1)
|
||||
i2_logml <- POP_LOGML[i2]
|
||||
|
||||
|
|
@ -81,7 +81,7 @@ laskeMuutokset <- function(ind, globalRows, data, adjprior, priorTerm) {
|
|||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] - repmat(diffInSumCounts, c(ni2, 1))
|
||||
|
||||
muutokset[i2] <- new_i1_logml - i1_logml + new_i2_logml - i2_logml
|
||||
LOGDIFF[ind, ] = muutokset
|
||||
LOGDIFF[ind, ] <- muutokset
|
||||
return(list(muutokset = muutokset, diffInCounts = diffInCounts))
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -5,6 +5,7 @@
|
|||
#' @return Either a list or a vector
|
||||
#' @author Waldir Leoncio
|
||||
min_MATLAB <- function(X, indices = TRUE) {
|
||||
if (!is(X, "matrix")) X <- as.matrix(X)
|
||||
mins <- apply(X, 2, min)
|
||||
idx <- sapply(seq_len(ncol(X)), function(x) match(mins[x], X[, x]))
|
||||
if (indices) {
|
||||
|
|
@ -21,6 +22,7 @@ min_MATLAB <- function(X, indices = TRUE) {
|
|||
#' @return Either a list or a vector
|
||||
#' @author Waldir Leoncio
|
||||
max_MATLAB <- function(X, indices = TRUE) {
|
||||
if (!is(X, "matrix")) X <- as.matrix(X)
|
||||
maxs <- apply(X, 2, max)
|
||||
idx <- sapply(seq_len(ncol(X)), function(x) match(maxs[x], X[, x]))
|
||||
if (indices) {
|
||||
|
|
|
|||
|
|
@ -15,6 +15,12 @@ repmat <- function (mx, n) {
|
|||
if (length(n) > 3) warning("Extra dimensions of n ignored")
|
||||
if (!is(mx, "matrix")) mx <- t(as.matrix(mx))
|
||||
if (length(n) == 1) n <- rep(n, 2)
|
||||
if (any(n == 0)) {
|
||||
n_zero <- which(n == 0)
|
||||
out_dim <- dim(mx)
|
||||
out_dim[n_zero] <- 0
|
||||
return(array(dim=out_dim))
|
||||
}
|
||||
|
||||
# Replicating cols
|
||||
out <- mx_col <- matrix(rep(mx, n[2]), nrow(mx))
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,14 +1,13 @@
|
|||
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]
|
||||
PARTITION[ind] <- i2
|
||||
|
||||
COUNTS[, , i1] <- COUNTS[, , i1] - diffInCounts
|
||||
COUNTS[, , i2] <- COUNTS[, , i2] + diffInCounts
|
||||
SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - sum[diffInCounts]
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + sum[diffInCounts]
|
||||
SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - colSums(diffInCounts)
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + colSums(diffInCounts)
|
||||
|
||||
POP_LOGML[c(i1, i2)] <- computePopulationLogml(
|
||||
c(i1, i2), adjprior, priorTerm
|
||||
|
|
@ -28,8 +27,8 @@ updateGlobalVariables2 <- function(i1, i2, diffInCounts, adjprior, priorTerm) {
|
|||
|
||||
COUNTS[, , i1] <- COUNTS[, , i1] - diffInCounts
|
||||
COUNTS[, , i2] <- COUNTS[, , i2] + diffInCounts
|
||||
SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - sum[diffInCounts]
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + sum[diffInCounts]
|
||||
SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - colSums(diffInCounts)
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + colSums(diffInCounts)
|
||||
|
||||
POP_LOGML[i1] <- 0
|
||||
POP_LOGML[i2] <- computePopulationLogml(i2, adjprior, priorTerm)
|
||||
|
|
@ -51,8 +50,8 @@ updateGlobalVariables3 <- function(
|
|||
|
||||
COUNTS[, , i1] <- COUNTS[, , i1] - diffInCounts
|
||||
COUNTS[, , i2] <- COUNTS[, , i2] + diffInCounts
|
||||
SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - sum[diffInCounts]
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + sum[diffInCounts]
|
||||
SUMCOUNTS[i1, ] <- SUMCOUNTS[i1, ] - colSums(diffInCounts)
|
||||
SUMCOUNTS[i2, ] <- SUMCOUNTS[i2, ] + colSums(diffInCounts)
|
||||
|
||||
POP_LOGML[c(i1, i2)] <- computePopulationLogml(
|
||||
c(i1, i2), adjprior, priorTerm
|
||||
|
|
|
|||
|
|
@ -4,13 +4,16 @@
|
|||
\alias{cell}
|
||||
\title{Cell array}
|
||||
\usage{
|
||||
cell(n, sz = c(n, n), ...)
|
||||
cell(n, sz = c(n, n), expandable = FALSE, ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{n}{a the first dimension (or both, if sz is not passed)}
|
||||
|
||||
\item{sz}{the second dimension (or 1st and 2nd, if not passed)}
|
||||
|
||||
\item{expandable}{if TRUE, output is a list (so it can take different
|
||||
lengths)}
|
||||
|
||||
\item{...}{Other dimensions}
|
||||
}
|
||||
\value{
|
||||
|
|
|
|||
|
|
@ -4,10 +4,12 @@
|
|||
\alias{find}
|
||||
\title{Find indices and values of nonzero elements}
|
||||
\usage{
|
||||
find(x)
|
||||
find(x, sort = TRUE)
|
||||
}
|
||||
\arguments{
|
||||
\item{x}{object or logic operation on an object}
|
||||
|
||||
\item{sort}{sort output?}
|
||||
}
|
||||
\description{
|
||||
Emulates behavior of `find`
|
||||
|
|
|
|||
|
|
@ -1,10 +1,42 @@
|
|||
context("Auxiliary functions to greedyMix")
|
||||
|
||||
baps_diploid <- read.delim(
|
||||
"inst/ext/ExamplesDataFormatting/Example data in BAPS format for clustering of diploid individuals.txt",
|
||||
sep = " ",
|
||||
header = FALSE
|
||||
)
|
||||
|
||||
handleData(baps_diploid)$newData
|
||||
|
||||
test_that("handleData works as expected", {
|
||||
data_obs <- handleData(baps_diploid)$newData
|
||||
data_exp <- matrix(
|
||||
c(
|
||||
-9, 1, 2, 1, 1, 1, 2, 1, 2, 2, 1,
|
||||
-9, 1, 1, 2, 2, 2, 1, 1, 1, 2, 1,
|
||||
3, 2, 2, 3, 2, -9, 3, 1, 2, 1, 2,
|
||||
2, 1, 2, 1, 2, -9, 1, 1, 1, 1, 2,
|
||||
3, 1, 1, 1, 2, 1, 1, 2, -9, 1, 3,
|
||||
3, 1, 2, 1, 1, 1, 2, 1, -9, 2, 3,
|
||||
1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 4,
|
||||
3, 2, 2, 3, 2, 2, 3, 1, 2, 1, 4,
|
||||
2, 1, 2, 1, -9, 1, 1, 1, 1, 1, 5,
|
||||
3, 1, 1, 1, -9, 1, 1, 2, 1, 1, 5
|
||||
),
|
||||
nrow = 10, byrow = TRUE
|
||||
)
|
||||
colnames(data_exp) <- colnames(data_obs)
|
||||
expect_equal(data_obs, data_exp)
|
||||
})
|
||||
|
||||
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
|
||||
|
||||
context("Linkage")
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue