pegas: cophenetic.haploNet – R documentation

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cophenetic.haploNet

Cophenetic Matrix on Haplotype Networks

Description

This function calculates the cophenetic distance on a network. The output can be used to find nodes with short distances to most nodes.

Usage

## S3 method for class 'haploNet'
cophenetic(x)

Arguments

`x`	an object of class `"haploNet"`.

Details

The results of the function are likely to be approximate in most cases with reticulations in the network. In the case of MSTs, the results are exact.

Value

a numeric matrix with colnames and rownames set to the labels of the network nodes.

Author(s)

Emmanuel Paradis

Examples

example(mst)
coph <- cophenetic(r)
rowSums(coph)

pegas

Population and Evolutionary Genetics Analysis System

v1.0

GPL (>= 2)

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Thibaut Jombart [aut, cph] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>), Brian Knaus [aut, cph] (<https://orcid.org/0000-0003-1665-4343>), Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Alastair Potts [aut, cph] (<https://orcid.org/0000-0003-0919-7279>), David Winter [aut, cph] (<https://orcid.org/0000-0002-6165-0029>)

Initial release

2021-04-08