combine.4thcorner {ade4} | R Documentation |
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 |
obj2 |
an object created with |
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.method.D |
a string indicating a method for multiple
adjustment used for output tabD/tabD2, see |
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.
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")