minpermute {codep}

Number of Permutations for MCA

Description

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

Usage

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

Arguments

alpha

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

nbtest

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

margin

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

ru

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

Details

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.

Value

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

Author(s)

Guillaume Guenard and Pierre Legendre, Bertrand Pages Maintainer: Guillaume Guenard <[e-mail]>

References

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

permute.cdp

Examples

## 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)