vegan (version 1.15-0)

add1.cca: Add or Drop Single Terms to a Constrained Ordination Model

Description

Compute all single terms that can be added or dropped from a constrained ordination model.

Usage

## S3 method for class 'cca':
add1(object, scope, test = c("none", "permutation"),
    pstep = 100, perm.max = 200, ...)
## S3 method for class 'cca':
drop1(object, scope, test = c("none", "permutation"), 
    pstep = 100, perm.max = 200, ...)

Arguments

object

A constrained ordination object from cca, rda or capscale.

scope

A formula giving the terms to be considered for adding or dropping; see add1 for details.

test

Should a permutation test added using anova.cca.

pstep

Number of permutations in one step, passed as argument step to anova.cca.

perm.max

Maximum number of permutation in anova.cca.

...

Other arguments passed to add1.default, drop1.default, and anova.cca.

Value

• Returns a similar object as add1 and drop1.

Details

With argument test = "none" the functions will only call add1.default or drop1.default. With argument test = "permutation" the functions will add test results from anova.cca. Function drop1.cca will call anova.cca with argument by = "margin". Function add1.cca will implement a test for single term additions that is not directly available in anova.cca.

Functions are used implicity in step. The deviance.cca and deviance.rda used in step have no firm basis, and setting argument test = "permutation" may help in getting useful insight into validity of model building. Meticulous use of add1.cca and drop1.cca will allow more judicious model building.

The default perm.max is set to a low value, because permutation tests can take a long time. It should be sufficient to give a impression on the significances of the terms, but higher values of perm.max should be used if $P$ values really are important.

See Also

add1, drop1 and anova.cca for basic methods. You probably need these functions with step. Functions deviance.cca and extractAIC.cca are used to produce the other arguments than test results in the output. Functions cca, rda and capscale produce result objects for these functions.

Examples

data(varespec)
data(varechem)
step(rda(varespec ~  1, varechem), reformulate(names(varechem)), test="perm")