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")

Value

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

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.

Author

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

Examples

Run this code

  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)