communities: Construct communities from individuals

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

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 [e-mail] https://www.unibo.it/sitoweb/christian.hennig/en

See Also

communitydist

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 documentation built on Sept. 24, 2024, 5:07 p.m.