R/RcppExports.R

In Takkoona/sitePath: Phylogeny-based sequence clustering with site polymorphism

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

pairSimilarity <- function(seqIndex, alignedSeqs) {
    .Call('_sitePath_pairSimilarity', PACKAGE = 'sitePath', seqIndex, alignedSeqs)
}

getSimilarityMatrix <- function(alignedSeqs) {
    .Call('_sitePath_getSimilarityMatrix', PACKAGE = 'sitePath', alignedSeqs)
}

majorSNPtips <- function(alignedSeqs, siteIndices, minSNPnum) {
    .Call('_sitePath_majorSNPtips', PACKAGE = 'sitePath', alignedSeqs, siteIndices, minSNPnum)
}

terminalTipsBySim <- function(siteIndices, tipPaths, alignedSeqs, metricMatrix) {
    .Call('_sitePath_terminalTipsBySim', PACKAGE = 'sitePath', siteIndices, tipPaths, alignedSeqs, metricMatrix)
}

terminalTipsByDist <- function(siteIndices, tipPaths, alignedSeqs, metricMatrix) {
    .Call('_sitePath_terminalTipsByDist', PACKAGE = 'sitePath', siteIndices, tipPaths, alignedSeqs, metricMatrix)
}

mergePaths <- function(paths) {
    .Call('_sitePath_mergePaths', PACKAGE = 'sitePath', paths)
}

divergentNode <- function(paths) {
    .Call('_sitePath_divergentNode', PACKAGE = 'sitePath', paths)
}

getReference <- function(refSeq, gapChar) {
    .Call('_sitePath_getReference', PACKAGE = 'sitePath', refSeq, gapChar)
}

tableAA <- function(seqs, siteIndex) {
    .Call('_sitePath_tableAA', PACKAGE = 'sitePath', seqs, siteIndex)
}

minEntropyByInserting <- function(nodeSummaries, minEffectiveSize, searchDepth) {
    .Call('_sitePath_minEntropyByInserting', PACKAGE = 'sitePath', nodeSummaries, minEffectiveSize, searchDepth)
}

minEntropyByDeleting <- function(nodeSummaries, minEffectiveSize, searchDepth) {
    .Call('_sitePath_minEntropyByDeleting', PACKAGE = 'sitePath', nodeSummaries, minEffectiveSize, searchDepth)
}

minEntropyByComparing <- function(nodeSummaries, minEffectiveSize, searchDepth) {
    .Call('_sitePath_minEntropyByComparing', PACKAGE = 'sitePath', nodeSummaries, minEffectiveSize, searchDepth)
}