procuste.rtest: Monte-Carlo Test on the sum of the singular values of a...

In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

Description

performs a Monte-Carlo Test on the sum of the singular values of a procustean rotation.

Usage

procuste.rtest(df1, df2, nrepet = 99)

Arguments

df1	a data frame
df2	a data frame
nrepet	the number of permutations

Value

returns a list of class rtest

Author(s)

Daniel Chessel
Anne B Dufour [e-mail]

References

Jackson, D.A. (1995) PROTEST: a PROcustean randomization TEST of community environment concordance. Ecosciences, 2, 297–303.

Examples

data(doubs)
pca1 <- dudi.pca(doubs$env, scal = TRUE, scann = FALSE)
pca2 <- dudi.pca(doubs$fish, scal = FALSE, scann = FALSE)
proc1 <- procuste(pca1$tab, pca2$tab)
protest1 <- procuste.rtest(pca1$tab, pca2$tab, 999)
protest1
plot(protest1)

Example output

Monte-Carlo test
Call: procuste.rtest(df1 = pca1$tab, df2 = pca2$tab, nrepet = 999)

Observation: 0.6562 

Based on 999 replicates
Simulated p-value: 0.001 
Alternative hypothesis: greater 

    Std.Obs Expectation    Variance 
6.348419665 0.343752013 0.002422279 

ade4 documentation built on May 2, 2019, 5:50 p.m.