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Minor changes for clean build

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This commit is contained in:
Waldir Leoncio 2020-03-18 15:02:38 +01:00
parent 7ad4fc43df
commit 1e5fa0ea91
10 changed files with 34 additions and 9 deletions
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17
R/admix1.R
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@ -4,6 +4,11 @@
#' will the required variables be retrieved from the record fields?
#' `tietue`should contain the following elements: PARTITION, COUNTS, SUMCOUNTS,
#' alleleCodes, adjprior, popnames, rowsFromInd, data, npops, noalle
#' @param tietue tietue
#' @param PARTITION PARTITION
#' @param COUNTS COUNTS
#' @param SUMCOUNTS SUMCOUNTS
#' @importFrom methods is
#' @export
admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
COUNTS = matrix(NA, 0, 0), SUMCOUNTS = NA) {
@ -20,7 +25,7 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
cat('---------------------------------------------------\n');
message('Reading mixture result from: ', pathname_filename, '...')
}
sys.sleep(0.0001) #ASK: what for?
Sys.sleep(0.0001) #ASK: what for?
# ASK: what is this supposed to do? What do graphic obj have to do here?
# h0 = findobj('Tag','filename1_text');
@ -79,7 +84,7 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
),
definput = 5
)
alaRaja <- as.num(answers)
alaRaja <- as.numeric(answers)
npops <- poistaLiianPienet(npops, rowsFromInd, alaRaja)
nloci <- size(COUNTS, 2)
@ -116,7 +121,7 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
# Yksil?on outlier
} else if (PARTITION[ind] != 0) {
if (PARTITION[ind] > 0) {
osuusTaulu(PARTITION[ind]) <- 1
osuusTaulu[PARTITION[ind]] <- 1
} else {
# Yksilöt, joita ei ole sijoitettu mihinkään koriin.
arvot <- zeros(1, npops)
@ -181,12 +186,12 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
omaFreqs <- computePersonalAllFreqs(
ind, data, allfreqs, rowsFromInd
)
osuusTaulu = zeros(1, npops)
osuusTaulu <- zeros(1, npops)
if (PARTITION[ind] == 0) {
# Yksil?on outlier
} else if (PARTITION[ind] != 0) {
if (PARTITION[ind] > 0) {
osuusTaulu(PARTITION[ind]) <- 1
osuusTaulu[PARTITION[ind]] <- 1
} else {
# Yksilöt, joita ei ole sijoitettu mihinkään koriin.
arvot <- zeros(1, npops)
@ -388,7 +393,7 @@ admix1 <- function(tietue, PARTITION = matrix(NA, 0, 0),
}
}
if (!isstruct(tietue)) {
if (!is(tietue, "list")) {
c$proportionsIt <- proportionsIt
c$pvalue <- uskottavuus # Added by Jing
c$mixtureType <- 'admix' # Jing

1
R/find.R
View file

@ -1,5 +1,6 @@
#' @title Find indices and values of nonzero elements
#' @description Emulates behavior of `find`
#' @param x object or logic operation on an object
find <- function(x) {
if (is.logical(x)) {
return(which(x))

2
R/inputdlg.R
View file

@ -1,7 +1,7 @@
#' @title Gather user input
#' @description Replicates the functionality of the homonymous function in Matlab (sans dialog box)
#' @param prompt Text field with user instructions
#' @param dim number of dimensions in the answwers
#' @param dims number of dimensions in the answwers
#' @param definput default value of the input
#' @export
inputdlg <- function(prompt, definput=NULL, dims=1) {

2
R/noIndex.R
View file

@ -3,6 +3,8 @@
#' @details As input, this function takes two variables from a mixture/admixture
#' result structure.
#' @return puredata: a data contains no index column.
#' @param data data
#' @param noalle noalle
#' @export
noIndex <- function (data, noalle) {
limit <- ifelse(is(noalle, "matrix"), ncol(noalle), length(noalle))