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Fixed handling of global

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This commit is contained in:
Waldir Leoncio 2021-01-15 09:36:50 +01:00
parent d47b84fb55
commit 0de7026430
4 changed files with 24 additions and 13 deletions
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9
R/computePersonalAllFreqs.R
View file

@ -10,11 +10,14 @@
#' @export #' @export
computePersonalAllFreqs <- function(ind, data, allFreqs, rowsFromInd) { computePersonalAllFreqs <- function(ind, data, allFreqs, rowsFromInd) {
nloci <- ifelse(is.na(dim(COUNTS)[2]), 1, dim(COUNTS)[2]) if (is.null(dim(COUNTS))) {
npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3]) nloci <- npops <- 1
} else {
nloci <- ifelse(is.na(dim(COUNTS)[2]), 1, dim(COUNTS)[2])
npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
}
rows <- as.matrix(t(data))[computeRows(rowsFromInd, ind, 1), , drop = FALSE] rows <- as.matrix(t(data))[computeRows(rowsFromInd, ind, 1), , drop = FALSE]
omaFreqs <- zeros(npops, rowsFromInd * nloci) omaFreqs <- zeros(npops, rowsFromInd * nloci)
pointer <- 1 pointer <- 1
for (loc in 1:dim(rows)[2]) { for (loc in 1:dim(rows)[2]) {

6
R/laskeMuutokset12345.R
View file

@ -9,7 +9,11 @@
#' @param logml log maximum likelihood #' @param logml log maximum likelihood
#' @export #' @export
laskeMuutokset4 <- function (osuus, osuusTaulu, omaFreqs, logml) { laskeMuutokset4 <- function (osuus, osuusTaulu, omaFreqs, logml) {
npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3]) if (is.null(dim(COUNTS))) {
npops <- 1
} else {
npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
}
notEmpty <- which(osuusTaulu > 0.005) notEmpty <- which(osuusTaulu > 0.005)
muutokset <- zeros(npops) muutokset <- zeros(npops)
empties <- !notEmpty empties <- !notEmpty

18
R/suoritaMuutos.R
View file

@ -5,14 +5,18 @@
#' @param indeksi index #' @param indeksi index
#' @export #' @export
suoritaMuutos <- function (osuusTaulu, osuus, indeksi) { suoritaMuutos <- function (osuusTaulu, osuus, indeksi) {
npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3]) if (is.null(dim(COUNTS))) {
npops <- 1
} else {
npops <- ifelse(is.na(dim(COUNTS)[3]), 1, dim(COUNTS)[3])
}
i1 <- indeksi %% npops i1 <- indeksi %% npops
if (is.na(i1) | i1 == 0) i1 <- npops if (is.na(i1) | i1 == 0) i1 <- npops
i2 <- ceiling(indeksi / npops) i2 <- ceiling(indeksi / npops)
osuusTaulu[i1] <- osuusTaulu[i1] - osuus osuusTaulu[i1] <- osuusTaulu[i1] - osuus
osuusTaulu[i2] <- osuusTaulu[i2] + osuus osuusTaulu[i2] <- osuusTaulu[i2] + osuus
return (osuusTaulu) return (osuusTaulu)
} }