ade4: combine.4thcorner – R documentation

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combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Description

Functions to combine and adjust the outputs of the fourthcorner and randtest.rlq functions created using permutational models 2 and 4 (sequential approach).

Usage

combine.randtest.rlq(obj1, obj2, ...)
combine.4thcorner(four1,four2)
p.adjust.4thcorner(x, p.adjust.method.G = p.adjust.methods,
p.adjust.method.D = p.adjust.methods, p.adjust.D = c("global",
"levels"))

Arguments

`four1`	an object of the class 4thcorner created with modeltype = 2 (or 4)
`four2`	an object of the class 4thcorner created with modeltype = 4 (or 2)
`obj1`	an object created with `randtest.rlq` and modeltype = 2 (or 4)
`obj2`	an object created with `randtest.rlq` and modeltype = 4 (or 2)
`x`	an object of the class 4thcorner
`p.adjust.method.G`	a string indicating a method for multiple adjustment used for output tabG, see `p.adjust.methods` for possible choices
`p.adjust.method.D`	a string indicating a method for multiple adjustment used for output tabD/tabD2, see `p.adjust.methods` for possible choices
`p.adjust.D`	a string indicating if multiple adjustment for tabD/tabD2 should be done globally or only between levels of a factor ("levels", as in the original paper of Legendre et al. 1997)
`...`	further arguments passed to or from other methods

Details

The functions combines the outputs of two objects (created by fourthcorner and randtest.rlq functions) as described in Dray and Legendre (2008) and ter Braak et al (2012).

Value

The functions return objects of the same class than their argument. They simply create a new object where pvalues are equal to the maximum of pvalues of the two arguments.

Author(s)

Stéphane Dray stephane.dray@univ-lyon1.fr

References

Dray, S. and Legendre, P. (2008) Testing the species traits-environment relationships: the fourth-corner problem revisited. Ecology, 89, 3400–3412.

ter Braak, C., Cormont, A., and Dray, S. (2012) Improved testing of species traits-environment relationships in the fourth corner problem. Ecology, 93, 1525–1526.

Examples

data(aravo)
four2 <- fourthcorner(aravo$env, aravo$spe, aravo$traits, nrepet=99,modeltype=2)
four4 <- fourthcorner(aravo$env, aravo$spe, aravo$traits, nrepet=99,modeltype=4)
four.comb <- combine.4thcorner(four2,four4)
## or directly :
## four.comb <- fourthcorner(aravo$env, aravo$spe, aravo$traits, nrepet=99,modeltype=6)
summary(four.comb)
plot(four.comb, stat = "G")

ade4

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release