ecos_prepare_by_phylo: Prepare counts data for phylogenetically collapsed species

In kkdey/ecostructure: Visualizing Structure in ecological site-species abundance data

Description

Starting from a taxonomic species abundance matrix, produces a new matrix, with features now collpased vesions of the species where the collapsing is done by a phylogenetic tree structure.

Usage

ecos_prepare_by_phylo(dat, tree, collapse_at)

Arguments

tree	The phylogenetic tree structure on the species or the column features of the counts matrix. Should be of the form .tre.
collapse_at	The point on the tree at which to collapse the tree
counts	The abundance counts matrix with samples/sites along the rows and the species/features along the columns.

Value

Returns a counts matrix with the features being the phylogenetically collapsed species from the original data based on the tree structure.

kkdey/ecostructure documentation built on Jan. 26, 2021, 4:10 p.m.