minpermute: Number of Permutations for MCA

View source: R/minpermute.R

minpermuteR Documentation

Number of Permutations for MCA


Calculates the number of permutations suitable for testing Multiscale Codependence Analysis.


minpermute(alpha, nbtest, margin = 1, ru = 3)



The familywise type I error threshold allowable for the complete analysis.


The number of test performed (the number of eigenvectors in the 'mem' object in the case of MCA).


A margin allowed for the number of permutation. Default value: 1.


The magnitude of the round-up to apply to the number of permutations.


This function calculate the number of permutations for use with permute.cdp. Argument margin allows to apply a safe margin to the number of permutations. The minimal suitable value for this parameter is 1. Argument ru allows one to round-up the number of permutations. A value of 0 implies no round-up, a value of 1 a round-up to the next ten, 2 a round-up to the next hundred, and so on. Function minpermute is called internally by permute.cdp in case permute = NA. In that case, the margin is set to 10 (margin = 10) and the outcome is rounded-up to the next thousand (ru = 3). This function is meant for users that wish to apply their own margins and round-up factors to calculate the number of permutations for use with permute.cdp.


The minimum number of permutation to be used for permute.cdp.


Guillaume Guenard and Pierre Legendre, Bertrand Pages Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>


Guénard, G., Legendre, P., Boisclair, D., and Bilodeau, M. 2010. Multiscale codependence analysis: an integrated approach to analyse relationships across scales. Ecology 91: 2952-2964

See Also



## For a 5\% threshold under 50 tests.
minpermute(alpha = 0.05, nbtest=50)

## Allowing more margin (implies more computation time).
minpermute(alpha = 0.05, nbtest=50, margin=10, ru=3)

guenardg/codep documentation built on April 15, 2023, 6:47 a.m.