max/ourMELONS
1
0
Fork 0
Code Issues 1 Pull requests Projects Releases Packages Wiki Activity Actions

Fixed calculation of ninds ekat (#24)

Browse source
This commit is contained in:
Waldir Leoncio 2024-03-25 16:04:11 +01:00
parent 530442487f
commit f361975254
1 changed files with 4 additions and 5 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

9
R/greedyMix.R
View file

@ -2,7 +2,6 @@
#' @param data data file #' @param data data file
#' @param format Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop" #' @param format Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop"
#' @param partitionCompare a list of partitions to compare #' @param partitionCompare a list of partitions to compare
#' @param ninds number of individuals
#' @param npops number of populations #' @param npops number of populations
#' @param counts counts #' @param counts counts
#' @param sumcounts sumcounts #' @param sumcounts sumcounts
@ -23,7 +22,7 @@
#' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS") #' data <- system.file("extdata", "FASTA_clustering_haploid.fasta", package = "rBAPS")
#' greedyMix(data, "fasta") #' greedyMix(data, "fasta")
greedyMix <- function( greedyMix <- function(
data, format = gsub("^.*\\.", "", data), partitionCompare = NULL, ninds = 1L, npops = 1L, data, format = gsub("^.*\\.", "", data), partitionCompare = NULL, npops = 1L,
counts = NULL, sumcounts = NULL, max_iter = 100L, alleleCodes = NULL, counts = NULL, sumcounts = NULL, max_iter = 100L, alleleCodes = NULL,
inp = NULL, popnames = NULL, fixedK = FALSE, verbose = FALSE inp = NULL, popnames = NULL, fixedK = FALSE, verbose = FALSE
) { ) {
@ -46,10 +45,10 @@ greedyMix <- function(
) )
} }
# Generating partition summary =============================================== # Generating partition summary ===============================================
ekat <- seq(1L, c[["rowsFromInd"]], ninds * c[["rowsFromInd"]]) # ekat = (1:rowsFromInd:ninds*rowsFromInd)'; ninds <- length(unique(data$data[, ncol(data$data)]))
c[["rows"]] <- c(ekat, ekat + c[["rowsFromInd"]] - 1L) # c.rows = [ekat ekat+rowsFromInd-1] ekat <- seq(1L, ninds * c[["rowsFromInd"]], c[["rowsFromInd"]])
c[["rows"]] <- cbind(ekat, ekat + c[["rowsFromInd"]] - 1L)
logml_npops_partitionSummary <- indMixWrapper(c, npops, counts, sumcounts, max_iter, fixedK, verbose) logml_npops_partitionSummary <- indMixWrapper(c, npops, counts, sumcounts, max_iter, fixedK, verbose)
logml <- logml_npops_partitionSummary[["logml"]] logml <- logml_npops_partitionSummary[["logml"]]
npops <- logml_npops_partitionSummary[["npops"]] npops <- logml_npops_partitionSummary[["npops"]]