prabclus (version 2.0-2)

hprabclust: Clustering of species ranges from presence-absence matrices (hierarchical methods)

Description

Clusters a presence-absence matrix object by taking the 'h-cut'-partition of a hierarchical clustering and declaring all members of too small clusters as 'noise' (this gives a distance-based clustering method, which estimates the number of clusters and allows for noise/non-clustered points). Note that this is experimental and up to now, the prabclust-solutions have been more convincing for all data sets we have tested. Note: Data formats are described on the prabinit help page. You may also consider the example datasets kykladspecreg.dat and nb.dat. Take care of the parameter rows.are.species of prabinit.

Usage

hprabclust(prabobj, cutdist=0.4, cutout=cutdist,
                        method="complete", nnout=2)

Arguments

prabobj

object of class prab as generated by prabinit. Presence-absence data to be analyzed.

cutdist

non-negative integer. Cutoff distance to determine the partition, see cutree.

cutout

non-negative integer. Points that have at most nnout distances smaller or equal than cutout are treated as noise.

method

string. Clustering method, see hclust.

nnout

non-negative integer. Members of clusters with less or equal than nnout points or that have less or equal than nnout neighbors closer than cutout are treated as noise.

Value

• hprabclust generates an object of class comprabclust. This is a list with components
• clustering
  vector of integers indicating the cluster memberships of the species (cutout-outliers are noise, but small clusters are allowed). Noise can be recognized by output component symbols.
• rclustering
  vector of integers indicating the cluster memberships of the species, noise as described under nnout. Noise can be recognized by output component symbols.
• cutdist
  see above.
• cutout
  see above.
• nnout
  see above.
• noisen
  number of points minus cutout-outliers.
• symbols
  vector of characters corresponding to rclustering, but estimated noise by "N".
• hclustering
  output of hclust.

See Also

hclust, cutree, prabclust.

Examples

data(kykladspecreg)
data(nb)
data(waterdist)
x <- prabinit(prabmatrix=kykladspecreg, neighborhood=nb,
              geodist=waterdist, distance="geco")
hprabclust(x)