ordtest: Ordination Distribution Test

In labdsv: Ordination and Multivariate Analysis for Ecology

Ordination Distribution Test

Description

Testing the distribution of points in an ordination

Usage

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

Arguments

ord	an object of class ‘dsvord’
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 iterations to perform to establish p-values

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.

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

Author(s)

David W. Roberts [e-mail]

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

labdsv documentation built on April 10, 2023, 5:08 p.m.