combine.4thcorner: Functions to combine and adjust the outputs 3-table methods In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

 combine.4thcorner 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)
"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.

`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")

```

ade4 documentation built on Feb. 16, 2023, 7:58 p.m.