R/RcppExports.R

In MSCquartets: Analyzing Gene Tree Quartets under the Multi-Species Coalescent

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# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

#' Build quartet table from distances
#'
#' This is a C++ function, called from quartetTable, to fill in the quartet counts.
#' From a list of topological distance matrices (1 for each gene tree) it determines all
#' gene quartets. It is not intended to be used as a stand-alone function, and hence not fully
#' documented. The faster looping in C++ over R gives substantial time improvements
#'
#' @param dList a list of distance matrices
#' @param M number of sets of 4 taxa
#' @param nt number of gene trees/distance matrices
#' @param Q matrix to fill out as table of quartet counts
#' @param random if 0 compute for all sets of 4 taxa, otherwise for M random ones
#' @param progressbar if TRUE, display progress bar
#' @seealso \code{\link{quartetTable}}, \code{\link{quartetTableParallel}}
#'
#' @export
quartetTallyCpp <- function(dList, M, nt, Q, random, progressbar = FALSE) {
    .Call('_MSCquartets_quartetTallyCpp', PACKAGE = 'MSCquartets', dList, M, nt, Q, random, progressbar)
}

#' Initialize vector of B quartets
#'
#' This is a C++ function, called from \code{TINNIKdist}, to initialize for
#' inference of B and T quartets.
#'
#' @param pTable a quartet table with p-values
#' @param m number of rows in pTable
#' @param alpha critical value for tree test
#' @param beta critical value for star tree test
#' @param colptest column with p value for tree test
#' @param colpstar column with p value for star tree test
#' @param Bquartets 0/1 vector encoding initial B quartets
#' @seealso \code{\link{quartetTable}}, \code{\link{quartetTableParallel}}
#'
#' @export
initBquartets <- function(pTable, m, alpha, beta, colptest, colpstar, Bquartets) {
    .Call('_MSCquartets_initBquartets', PACKAGE = 'MSCquartets', pTable, m, alpha, beta, colptest, colpstar, Bquartets)
}

#' Main loop of B-quartet inference
#'
#' This is a C++ function, called from \code{TINNIKdist}, to
#' infer B and T quartets.
#'
#' @param pTable a quartet table with p-values
#' @param C precomputed binomial coefficients
#' @param Cn4 precomputed binomial coefficient
#' @param n number of taxa
#' @param Bquartets 0/1 vector of initial Bquartets
#' @param L1 vector of recently inferred B quartets
#' @param lenL1 lnegth of L1
#' @param Nrule1 count of inference from rule 1
#' @param Nrule2 count of inference from rule 2
#' @param cuttops inferred cut topologies
#'
#' @seealso \code{\link{quartetTable}}, \code{\link{quartetTableParallel}}
#'
#' @export
BQinference <- function(pTable, C, Cn4, n, Bquartets, L1, lenL1, Nrule1, Nrule2, cuttops) {
    .Call('_MSCquartets_BQinference', PACKAGE = 'MSCquartets', pTable, C, Cn4, n, Bquartets, L1, lenL1, Nrule1, Nrule2, cuttops)
}