Pairwise comparisons of groups displayed on a factorial map

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Description

Performs pairwise comparisons between group levels with corrections for multiple testing. Tests are computed using factorfit.

Usage

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pairwise.factorfit(ord, fact, xax = 1, yax = 2, nperm = 999,
  p.method = "fdr", ...)

Arguments

ord

any multivariate analysis handled by MVA.scores.

fact

grouping factor.

xax

first axis of the factorial map.

yax

second axis of the factorial map.

nperm

number of permutations.

p.method

method for p-values correction. See help of p.adjust.

...

optional further agruments to MVA.scores.

Value

method

a character string giving the name of the test.

data.name

a character string giving the name(s) of the data and the number of permutations.

p.value

table of results.

p.adjust.method

method for p-values correction.

Author(s)

Maxime Herv<e9> <mx.herve@gmail.com>

See Also

factorfit

Examples

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require(vegan)
data(iris)

PCA <- rda(iris[,1:4])
MVA.plot(PCA,fac=iris$Species,col=1:3)

# Global test
envfit(PCA~Species,data=iris)

# Pairwise comparisons
# (not enough permutations here but faster to run)
pairwise.factorfit(PCA,iris$Species,nperm=49)

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