align_comm_V: Create phylogenetic var-cov matrix based on phylogeny and...
In daijiang/phyr: Model Based Phylogenetic Analysis

align_comm_V

R Documentation

Create phylogenetic var-cov matrix based on phylogeny and community data

Description

This function will remove species from community data that are not in the phylogeny. It will also remove tips from the phylogeny that are not in the community data. And then convert the phylogeny to a Var-cov matrix.

Usage

align_comm_V(comm, tree, prune.tree = FALSE, scale.vcv = TRUE)

Arguments

`comm`	A site by species data frame, with site names as row names.
`tree`	A phylogeny with "phylo" as class; or a phylogenetic var-covar matrix.
`prune.tree`	Whether to prune the tree first then use vcv.phylo function. Default is FALSE: use vcv.phylo first then subsetting the matrix.
`scale.vcv`	Whether to scale vcv to a correlation matrix.