indicspecies (version 1.6.7)

multipatt: Multi-level pattern analysis

Description

This function studies the association between species patterns and combinations of groups of sites.

Usage

multipatt(x, cluster, func = "IndVal.g", duleg=FALSE, restcomb=NULL, max.order = NULL, control=permControl(), print.perm=FALSE)

Value

An object of class multipatt with:funcThe name of the function used.combA matrix describing all the combinations studied.strA matrix the association strength for all combinations studied.AIf func = "IndVal" (or func = "IndVal.g") a matrix whose values are the "A" (or "A.g") component of indicator values. Otherwise this element is left as NULL.BIf func = "IndVal" (or func = "IndVal.g") a matrix whose values are the "B" component of indicator values. Otherwise this element is left as NULL.signData table with results of the best matching pattern, the association value and the degree of statistical significance of the association (i.e. p-values from permutation test). Note that p-values are not corrected for multiple testing.

encoding

UTF-8

Details

This function creates combinations of the input clusters and compares each combination with the species in the input matrix x. For each species it chooses the combination with a highest association value. Best matching patterns are tested for statistical significance of the associations. Four association indices are possible (some less than for strassoc): "IndVal", "IndVal.g", "r" and "r.g". Indicator value indices will return the pattern that better matches the species observed pattern, whereas correlation indices will return the pattern that creates a highest inside/outside difference. Details are given in De Cáceres{Caceres} et al. (2010). The user can restrict the combinations in three ways: (1) by using duleg=TRUE, which leads to consider single site-groups only; (2) by setting the maximum order of combinations using max.order; or (3) by using restcomb to restrict combinations at will. In order to carry out the third way, values in restcomb must be the indices of combinations that appear in the column index of object sign (see below). Complex permutation designs are allowed through the function permControl from package "permute".

References

De Cáceres{Caceres}, M. and Legendre, P. 2009. Associations between species and groups of sites: indices and statistical inference. Ecology 90(12): 3566-3574.

De Cáceres{Caceres}, M., Legendre, P., Moretti, M. 2010. Improving indicator species analysis by combining groups of sites. Oikos 119(10): 1674-1684.

Dufrêne{Dufrene}, M. and P. Legendre. 1997. Species assemblages and indicator species: The need for a flexible asymetrical approach. Ecological Monographs 67:345-366.

See Also

summary.multipatt, strassoc, signassoc, permControl

Examples

library(stats)

data(wetland) ## Loads species data

wetkm = kmeans(wetland, centers=3) ## Creates three clusters using kmeans

wetpt = multipatt(wetland, wetkm$cluster, control = permControl(nperm=999)) ## Runs the combination analysis using IndVal.g as statistic

summary(wetpt) ## Lists those species with significant association to one combination

summary(wetpt, indvalcomp=TRUE) ## Lists those species with significant association to one combination. Includes indval components