phyloWeights: Phylogenetic weights matrix

In fkeck/phylosignal: Exploring the Phylogenetic Signal in Continuous Traits

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

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

See Also

proxTips in adephylo.

fkeck/phylosignal documentation built on Oct. 15, 2023, 2:57 a.m.