paco (version 0.2.3)

PACo: Performs PACo/procustes analysis

Description

Performs PACo/procustes analysis

Usage

PACo(D, nperm = 1000, seed = NA, method = "r0", symmetric = FALSE, correction = "none")

Arguments

D

a list with the data

nperm

Number of permutations

seed

Seed if results need to be reproduced

method

The method to permute matrices with: "r0", "r1", "r2", "c0", "swap", "quasiswap", "backtrack", "tswap", "r00". See commsim for details

symmetric

Use symmetric Procrustes statistic

correction

Choose the method with which to correct negative eigenvalues in the internal call of add_pcoord ('none', cailliez', 'lingoes'). Default is 'none'.

Examples

data(gopherlice)
require(ape)
gdist <- cophenetic(gophertree)
ldist <- cophenetic(licetree)
D <- prepare_paco_data(gdist, ldist, gl_links)
D <- add_pcoord(D)
D <- PACo(D, nperm=10, seed=42, method="r0", correction='cailliez')
print(D$gof)