prabclus: alleledist – R documentation

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alleledist

Shared allele distance for diploid loci

Description

Shared allele distance for codominant markers (Bowcock et al., 1994). One minus proportion of alleles shared by two individuals averaged over loci (loci with missing values for at least one individual are ignored).

Usage

alleledist(allelelist,ni,np,count=FALSE)

Arguments

`allelelist`	a list of lists. In the "outer" list, there are `np` 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. Such a list can be constructed by `unbuild.charmatrix` out of the `charmatrix` component of an output object of `alleleinit`.
`ni`	integer. Number of individuals.
`np`	integer. Number of loci.
`count`	logical. If `TRUE`, the number of the individual to be processed is printed.

Value

A symmetrical matrix of shared allele distances between individuals.

Author(s)

Christian Hennig christian.hennig@unibo.it https://www.unibo.it/sitoweb/christian.hennig/en

References

Bowcock, A. M., Ruiz-Linares, A., Tomfohrde, J., Minch, E., Kidd, J. R., Cavalli-Sforza, L. L. (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368, 455-457.

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$nblist,distance="none")
  str(alleledist((unbuild.charmatrix(tai$charmatrix,50,13)),50,13))

prabclus

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

v2.3-2

GPL

Authors

Christian Hennig <christian.hennig@unibo.it>, Bernhard Hausdorf <Hausdorf@zoologie.uni-hamburg.de>

Initial release

2020-01-06