Ordination Distribution Test
Testing the distribution of points in an ordination
ordtest(ord, var, dim=1:ncol(ord$points), index = 'euclidean', nitr = 1000)
ord |
an object of class ‘dsvord’ |
var |
a logical or factor vector used to organize the calculation of within-set distances |
dim |
the number of dimensions to use in the calculation |
index |
the distance metric for the calculation of within-set distances. Currently only euclidean is accepted |
nitr |
the number of iterations to perform to establish p-values |
Calculates the sum of within-set pair-wise distances and compares to ‘nitr’ permutations of the same distribution to calculate the probability of observing clusters as tight as observed or tighter. The p-value is calculated by running nitr-1 permutations and counting the number of cases where the sum of pair-wise distances is as small as smaller than observed. That count is increased by one and divided by nitr to estimate p.
Produces a list with components:
obs |
the observed sum of within-set distances |
p |
the probability of obtaining a value that small |
reps |
the sum of within-set pairwise distances for all permutations |
data(bryceveg) data(brycesite) dis.bc <- dsvdis(bryceveg,'bray/curtis') pco.bc <- pco(dis.bc) plot(pco.bc) demo <- ordtest(pco.bc,brycesite$quad) demo$p
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