pairwise.factorfit function

Pairwise comparisons of groups displayed on a factorial map

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

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.

Returns

• 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 HERVE maxime.herve@univ-rennes1.fr

See Also

factorfit

Examples

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)