Analysis of community ecology data in R

TWINSPAN (hierarchical divisive classification)

Example 1: Modified TWINSPAN on Danube dataset

Run TWINSPAN example using package twinspanR¹⁾, which demonstrates application of the modified TWINSPAN on a classical Ellenberg's Danube meadow dataset. Results of TWINSPAN classification are then projected on DCA ordination diagram and compared with original classification into three vegetation types (plus one not-classified relevé) made by tabular sorting.

library (twinspanR)
library (vegan)
data (danube)
res <- twinspan (danube$spe, modif = TRUE, clusters = 4)
k <- cut (res)
dca <- decorana (danube$spe)
par (mfrow = c(1,2))
ordiplot (dca, type = 'n', display = 'si', main = 'Modified TWINSPAN')
points (dca, col = k)
for (i in c(1,2,4)) ordihull (dca, groups = k, show.group = i, col = i,
 draw = 'polygon', label = TRUE)
ordiplot (dca, type = 'n', display = 'si', main = 'Original assignment\n (Ellenberg 1954)')
points (dca, col = danube$env$veg.type)
for (i in c(1:3)) ordihull (dca, groups = danube$env$veg.type,
 show.group = unique (danube$env$veg.type)[i], col = i,
 draw = 'polygon', label = TRUE)

¹⁾

You would get the same result as the script below if you run example (twinspan) - this will run the example which comes with the help file of twinspan function (see the section Examples in ?twinspan).