unbuild.charmatrix: Internal: create allele list out of character matrix

In prabclus: Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data

Internal: create allele list out of character matrix

Description

Creates a list of lists, such as required by alleledist, from the charmatrix component of an alleleobject.

Usage

   unbuild.charmatrix(charmatrix,n.individuals,n.variables)

Arguments

charmatrix	matrix of characters in which there are two rows for every individual corresponding to the two alleles in every locus (column). Entries are allele codes but missing values are coded as NA.
n.individuals	integer. Number of individuals.
n.variables	integer. Number of loci.

Value

A list of lists. In the "outer" list, there are n.variables lists, one for each locus. In the "inner" list, for every individual there is a vector of two codes (typically characters, see alleleinit) for the two alleles in that locus.

Author(s)

Christian Hennig [e-mail] https://www.unibo.it/sitoweb/christian.hennig/en

See Also

alleleinit, build.charmatrix

Examples

  data(tetragonula)
  tnb <-
  coord2dist(coordmatrix=tetragonula.coord[1:50,],cut=50,file.format="decimal2",neighbors=TRUE)
  ta <- alleleconvert(strmatrix=tetragonula[1:50,])
  tai <- alleleinit(allelematrix=ta,neighborhood=tnb$nblist,distance="none")
  str(unbuild.charmatrix(tai$charmatrix,50,13)) 

prabclus documentation built on Sept. 24, 2024, 5:07 p.m.