prabclus: hprabclust – R documentation

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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. Often, the prabclust-solutions is more convincing due to higher flexibility of that method. However, hprabclust may be more stable sometimes.

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=1,
method="average", nnout=2, mdsplot=TRUE, mdsmethod="classical")

## S3 method for class 'comprabclust'
print(x, ...)

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.
`mdsplot`	logical. If `TRUE`, the cluster solution is plotted on the first two MDS dimensions, see `mdsmethod`.
`mdsmethod`	`"classical"`, `"kruskal"`, or `"sammon"`. The MDS method to transform the distances to data points. `"classical"` indicates metric MDS by function `cmdscale`, `"kruskal"` is non-metric MDS. Note that if `mdsmethod!="classical"` zero distances between different objects are replaced by the minimum of the nonzero distances divided by 10 (otherwise the MDS method would produce an error). Note that `mdsmethod` is ignored if `mdsplot=FALSE`.
`x`	`comprabclust`-object as generated by `hprabclus`.
`...`	necessary for print method.

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 is coded as 0.
`rclustering`	vector of integers indicating the cluster memberships of the species, noise as described under `nnout`. Noise is coded as 0.
`cutdist`	see above.
`method`	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"`.
`points`	numerical matrix. MDS configuration (if `mdsplot=TRUE`).
`call`	function call.

Author(s)

Christian Hennig christian.hennig@unibo.it https://www.unibo.it/sitoweb/christian.hennig/en

Examples

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

prabclus

Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data

v2.3-2

GPL

Authors

Christian Hennig <christian.hennig@unibo.it>, Bernhard Hausdorf <Hausdorf@zoologie.uni-hamburg.de>

Initial release

2020-01-06