prabclus: communities – R documentation

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communities

Construct communities from individuals

Description

Construct communities from individuals using geographical distance and hierarchical clustering. Communities are clusters of geographically close individuals, formed by hclust with specified distance cutoff.

Usage

communities(geodist,grouping=NULL,
                        cutoff=1e-5,method="single")

Arguments

`geodist`	`dist`-object or matrix of geographical distances between individuals.
`grouping`	something that can be coerced into a factor. Different groups indicated by `grouping` cannot be together in the same community. (If `NULL`, there is no constraint.)
`cutoff`	numeric; clustering distance cutoff value, passed on as parameter `h` to `cutree`. Note that if this is smaller than the smallest nonzero geographical distance, communities will be all sets of individuals that have zero geographical distance to each other.
`method`	`method`-parameter for `hclust`.

Value

Vector of community memberships for the individuals (integer numbers from 1 to the number of communities without interruption.

Author(s)

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

Examples

data(veronica)
  ver.geo <- coord2dist(coordmatrix=veronica.coord[1:90,],file.format="decimal2")
  species <-c(rep(1,64),rep(2,17),rep(3,9))
  communities(ver.geo,species)

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