labdsv (version 1.2-0)

ordtest: Ordination Distribution Test

Description

Testing the distribution of points in an ordination

Usage

ordtest(ord, var, dim=c(1:ncol(ord$points)), index = 'euclidean',
   nitr = 1000)

Arguments

ord

an object of class pca, pco, or nmds

var

a logical or factor vector used to organize the calculation of within-set distances

dim

the number of dimensions to use in the calculation

index

the distance metric for the calculation of within-set distances. Currently only euclidean is accepted

nitr

the number of iteration to perform to establish p-values

Value

• Produces a list with components:
• obs
  the observed sum of within-set distances
• p
  the probability of obtaining a value that small
• reps
  the sum of within-set pairwise distances for all permutations

Details

Calculates the sum of within-set pair-wise distances and compares to nitr permutations of the same distribution to calculate the probability of observing clusters as tight as observed or tighter. The p-value is calculated by running nitr-1 permutations and counting the number of cases where the sum of pair-wise distances is as small as smaller than observed. That count is increased by one and divided by nitr to estimate p.

References

http://ecology.msu.montana.edu/labdsv/R

See Also

anosim

Examples

data(bryceveg)
data(brycesite)
dis.bc <- dsvdis(bryceveg,'bray/curtis')
pco.bc <- pco(dis.bc)
plot(pco.bc)
demo <- ordtest(pco.bc,brycesite$quad)
demo$p