R: Return Procrustes residuals from a paco object

residuals_paco {paco} | R Documentation

## Return Procrustes residuals from a paco object

### Description

Takes the Procrustes object from `vegan::procrustes` of the global superimpostion and pulls out either the residual matrix of superimposition or the residual of each individual interaction (link between host and parasite).

### Usage

    residuals_paco(object, type = "interaction")

### Arguments

`object` | An obejct of class `procrustes` as returned from PACo (and internally the `vegan::procrustes` function). In a PACo output this is `D$proc`.
`type` | Character string. Whether the whole residual matrix (`matrix`) or the residuals per interaction (`interaction`) is desired.

### Value

If `type=interaction`, a named vector of the Procrustes residuals is returned where names are the interactions. If `type=matrix`, a matrix of residuals from Procrustes superimposition is returned.

### Examples

    data(gopherlice)
    library(ape)
    gdist <- cophenetic(gophertree)
    ldist <- cophenetic(licetree)
    D <- prepare_paco_data(gdist, ldist, gl_links)
    D <- add_pcoord(D, correction='cailliez')
    D <- PACo(D, nperm=100, seed=42, method='r0')
    residuals_paco(D$proc)

[Package paco version 0.3.2 Index]