minpermute: Number of permutations for MCA
In codep: Multiscale Codependence Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

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

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

`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.

This function calculate the number of permutations for use with permute.cdp. Parameter margin allows to apply a safe margin to the number of permutations. The minimal suitable value for this parameter is 1. Parameter 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 Guénard, Département des sciences biologiques, Université de Montréal, Montréal, Québec, Canada.

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

permute.cdp

# 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)