add_pcoord {paco}

Principal Coordinates analysis of phylogenetic distance matrices

Description

Translates the distance matrices of 'host' and 'parasite' phylogenies into Principal Coordinates, as needed for Procrustes superimposition.

Usage

add_pcoord(D, correction = "none")

Arguments

D

A list with objects H, P, and HP, as returned by paco::prepare_paco_data.

correction

In some cases, phylogenetic distance matrices are non-Euclidean which generates negative eigenvalues when those matrices are translated into Principal Coordinates. There are several methods to correct negative eigenvalues. Correction options available here are "cailliez", "lingoes", and "none". The "cailliez" and "lingoes" corrections add a constant to the eigenvalues to make them non-negative. Default is "none".

Value

The list that was input as the argument ‘D’ with four new elements; the Principal Coordinates of the ‘host’ distance matrix and the Principal Coordinates of the ‘parasite’ distance matrix, as well as, a ‘correction’ object stating the correction used for negative eigenvalues and a ‘note’ object stating whether or not negative eigenvalues were present and therefore corrected.

Note

To find the Principal Coordinates of each distance matrix, we internally a modified version of the function ape::pcoa that uses vegan::eigenvals and zapsmall

Examples

data(gopherlice)
library(ape)
gdist <- cophenetic(gophertree)
ldist <- cophenetic(licetree)
D <- prepare_paco_data(gdist, ldist, gl_links)
D <- add_pcoord(D)