R: Phylogenetic weights matrix

phyloWeights {phylosignal}

R Documentation

Phylogenetic weights matrix

Description

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

Usage

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":

\frac{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