combine.4thcorner: Functions to combine and adjust the outputs 3-table methods

In sdray/ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

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 [e-mail]

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.

See Also

rlq, fourthcorner, p.adjust.methods

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")

sdray/ade4 documentation built on March 30, 2024, 12:33 a.m.