Phylogenetic weights matrix

Description

This function can be used to compute a phylogenetic weights matrix with different methods.

Usage

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phyloWeights(tree, dist.phylo = "patristic", method = "lag-norm", mu = 0,
  sigma = 5, dmax = 10, alpha = 1, beta = 1)

Arguments

tree

a phylo, phylo4 or phylo4d object.

dist.phylo

a character string specifying the method used to compute phylogenetic distances. Available distances are "patristic","nNodes","Abouheif" and "sumDD". See Details.

method

a method to compute phylogenetic weights from phylogenetic distances. Available methods are "lag-norm", "clade", "inverse" and "exponential". See Details.

mu

a numeric value giving the mean of the distribution if method is lag-norm. This is a phylogenetic distance.

sigma

a numeric value giving the standard deviation of the distribution if method is lag-norm.

dmax

the maximum phylogenetic distance to use to delineate clades.

alpha

a numeric value giving the exponent to use if method is inverse.

beta

a numeric value giving the factor to use if method is exponential.

Details

Method "inverse":

w = 1/d^alpha

The phylogenetic distance matrix is computed internally using the function distTips from the package adephylo. See distTips for details about the methods.

Value

A square matrix of phylogenetic weights whose sums of rows is 1.

See Also

proxTips in adephylo.

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