chkdim.Add.fun

chkdim.Multiply.fun

construct.bigB.dPI

construct.dB.list.fun

final.BigMatB.fun

final.BigMatB.matC.fun

get.allpossROUTE.fun

get.BB.fun

get.deriBigMatB.fun

get.fullBB.fun

get.I.fun

get.ini.possHap.hapReserv.fun

get.matD.matEI.fun

get.medBB.skip.fun

get.preBB.skip.fun

get.step.mut.fun

get.subPI.fun

getBigMatB.fun

getI13.fun

getPIstar.fun

haplo.phase.known

haplo.score.RD.unphased.fun

I33Inv.fun

index.k.fun

zero.mat.fun

See <code>all.internal</code> for phyclust.<p></p><p>  <code>chkdim.Add.fun</code>,
  <code>chkdim.Multiply.fun</code>, <code>construct.bigB.dPI</code>,
  <code>construct.dB.list.fun</code>, <code>final.BigMatB.fun</code>,
  <code>final.BigMatB.matC.fun</code>, <code>get.allpossROUTE.fun</code>,
  <code>get.BB.fun</code>, <code>get.deriBigMatB.fun</code>,
  <code>get.fullBB.fun</code>, <code>get.I.fun</code>,
  <code>get.ini.possHap.hapReserv.fun</code>, <code>get.matD.matEI.fun</code>,
  <code>get.medBB.skip.fun</code>, <code>get.preBB.skip.fun</code>,
  <code>get.step.mut.fun</code>, <code>get.subPI.fun</code>,
  <code>getBigMatB.fun</code>, <code>getI13.fun</code>,
  <code>getPIstar.fun</code>, <code>haplo.phase.known</code>,
  <code>haplo.score.RD.unphased.fun</code>, <code>I33Inv.fun</code>,
  <code>index.k.fun</code>, <code>zero.mat.fun</code>.</p>

internal

all.internal.tzeng

Phylogenetic clustering (phyloclustering) is an
        evolutionary Continuous Time Markov Chain model-based approach
        to identify population structure from molecular data without
        assuming linkage equilibrium. It provides a convenient
        implementation of phyloclustering for DNA and SNP data, capable
        of clustering individuals into subpopulations and identifying
        molecular sequences representative of those subpopulations. It
        is designed in C for performance, interfaced with R for
        visualization, and incorporates other popular open source
        software, ms, seq-gen and Hap-Clustering for simulating data
        and additional analyses. See the phyclust website for more
        information, documentations and examples.

all.internal.tzeng: All internal functions of Tzeng's methods

Description

Arguments

References