permiv: Permutation of group membership for a single candidate...

In TITAN2: Threshold Indicator Taxa Analysis

Permutation of group membership for a single candidate partition

Description

Randomizes group assignments for all permutations based on ranked values of the environmental gradient, then calls the appropriate matrix-based IndVal function.

Usage

permiv(grp, spp, ivTot = ivTot, nPerm = 250)

Arguments

grp	A vector of binary (0,1) assignments indicating group membership for a single partition of nrows in 'spp' according to a ranks of an environmental variable.
spp	A site-by-taxon matrix of taxa counts at each sampling location.
ivTot	A logical indicating whether IndVal scores should be calculated using total relative abundance or the mean relative abundace originally proposed by Dufrene and Legendre (1997).
nPerm	The number of permutations to be performed.

Details

This function handles the randomization portion of the permutation procedure, and then serves as a wrapper for 'indvalp' and 'indvalps' (depending on the value of 'ivTot'), which estimate change-point distributions across all permutations. The output is the same as 'indvalp' and 'indvalps' because the function simply passes their products on.

Value

A matrix (ivmax) of IndVal maxima with nrow equal to the number of permutations and ncol equal to the number of taxa in 'spp'.

Author(s)

M. Baker and R. King

References

Dufrene, M. and P. Legendre. 1997. Species assemblages and indicator species: the need for a flexible asymmetrical approach. Ecol. Mon. 67:345-366.

Baker, ME and RS King. 2010. A new method for detecting and interpreting biodiversity and ecological community thresholds. Methods in Ecology and Evolution 1(1): 25:37.

See Also

indvalp(), indvalps(), getivz()

TITAN2 documentation built on Nov. 15, 2023, 1:09 a.m.