diff --git a/R/greedyMix.R b/R/greedyMix.R index c82f7e9..6715145 100644 --- a/R/greedyMix.R +++ b/R/greedyMix.R @@ -1,6 +1,20 @@ #' @title Clustering of individuals #' @param data data file #' @param format Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop" +#' @param partitionCompare a list of partitions to compare +#' @param ninds number of individuals +#' @param rowsFromInd a list of rows for each individual +#' @param noalle number of alleles +#' @param adjprior ajuster prior probabilities +#' @param npops number of populations +#' @param priorTerm prior terms +#' @param counts counts +#' @param sumcounts sumcounts +#' @param max_iter maximum number of iterations +#' @param alleleCodes allele codes +#' @param inp input file +#' @param popnames population names +#' @param fixedK if \code{TRUE}, the number of populations is fixed #' @param verbose if \code{TRUE}, prints extra output information #' @importFrom utils read.delim #' @importFrom vcfR read.vcfR @@ -33,7 +47,7 @@ greedyMix <- function( # Comparing partitions ======================================================= if (!is.null(partitionCompare)) { logmls <- comparePartitions( - data, nrows(data), partitionCompare[["partitions"]], ninds, rowsFromInd, + data, nrow(data), partitionCompare[["partitions"]], ninds, rowsFromInd, noalle, adjprior ) } diff --git a/man/greedyMix.Rd b/man/greedyMix.Rd index 7b01722..74242b8 100644 --- a/man/greedyMix.Rd +++ b/man/greedyMix.Rd @@ -7,17 +7,21 @@ greedyMix( data, format, - partitionCompare, - ninds, - rowsFromInd, - noalle, - adjprior, - priorTerm, - alleleCodesinp, - popnames, + partitionCompare = NULL, + ninds = NULL, + rowsFromInd = NULL, + noalle = NULL, + adjprior = NULL, + npops = 1L, + priorTerm = NULL, + counts = NULL, + sumcounts = NULL, + max_iter = 100L, + alleleCodes = NULL, + inp = NULL, + popnames = NULL, fixedK = FALSE, - partition_compare = FALSE, - verbose = TRUE + verbose = FALSE ) } \arguments{ @@ -25,6 +29,34 @@ greedyMix( \item{format}{Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop"} +\item{partitionCompare}{a list of partitions to compare} + +\item{ninds}{number of individuals} + +\item{rowsFromInd}{a list of rows for each individual} + +\item{noalle}{number of alleles} + +\item{adjprior}{ajuster prior probabilities} + +\item{npops}{number of populations} + +\item{priorTerm}{prior terms} + +\item{counts}{counts} + +\item{sumcounts}{sumcounts} + +\item{max_iter}{maximum number of iterations} + +\item{alleleCodes}{allele codes} + +\item{inp}{input file} + +\item{popnames}{population names} + +\item{fixedK}{if \code{TRUE}, the number of populations is fixed} + \item{verbose}{if \code{TRUE}, prints extra output information} } \description{