This function can be used to compute a phylogenetic weights matrix with different methods.
phyloWeights(
tree,
dist.phylo = "patristic",
method = "lag-norm",
mu = 0,
sigma = 5,
dmax = 10,
alpha = 1,
beta = 1
)A square matrix of phylogenetic weights whose sums of rows is 1.
a phylo, phylo4 or phylo4d object.
a character string specifying the method used to compute phylogenetic distances.
Available distances are "patristic","nNodes","Abouheif" and "sumDD".
See Details.
a method to compute phylogenetic weights from phylogenetic distances.
Available methods are "lag-norm", "clade", "inverse" and "exponential".
See Details.
a numeric value giving the mean of the distribution if method is lag-norm.
This is a phylogenetic distance.
a numeric value giving the standard deviation
of the distribution if method is lag-norm.
the maximum phylogenetic distance to use to delineate clades.
a numeric value giving the exponent to use if method is inverse.
a numeric value giving the factor to use if method is exponential.
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.
proxTips in adephylo.