R: Clustering of species ranges from presence-absence matrices...

hprabclust {prabclus} | R Documentation

## 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 chrish@stats.ucl.ac.uk http://www.homepages.ucl.ac.uk/~ucakche

### See Also

`hclust`, `cutree`, `prabclust`.

### Examples

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

[Package prabclus version 2.2-6 Index]