R: Principal Coordinates analysis of phylogenetic distance...

add_pcoord {paco} | R Documentation

## 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 two new elements; the Principal Coordinates of the ‘host’ distance matrix and the Principal Coordinates of the ‘parasite’ distance matrix.

### Note

To find the Principal Coordinates of each distance matrix, we internally use a function, `coordpcoa`, that is a modified version of `ape::pcoa`, using `vegan::eigenvals`.

### Examples

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

[Package paco version 0.3.2 Index]