pairwise.factorfit: Pairwise comparisons of groups displayed on a factorial map

In RVAideMemoire: Testing and Plotting Procedures for Biostatistics

Pairwise comparisons of groups displayed on a factorial map

Description

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

Usage

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 HERVE <[e-mail]>

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)

RVAideMemoire documentation built on Nov. 6, 2023, 5:07 p.m.