specgroups: Average within-group distances for given groups

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

Average within-group distances for given groups

Description

Generates average within-group distances (overall and group-wise) from a dissimilarity matrix and a given grouping.

Usage

  specgroups(distmat,groupvector, groupinfo) 

Arguments

distmat	dissimilarity matrix or dist-object.
groupvector	integer vector. For every row of distmat, a number indicating the group membership.
groupinfo	list with components lg (levels of groupvector), ng (number of groups), nsg (vector of group sizes).

Value

A list with parameters

overall	overall average within-groups dissimilarity.
gr	vector of group-wise average within-group dissimilarities (this will be NaN if the group size is only 1).

Author(s)

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

Examples

  options(digits=4)
  data(siskiyou)
  x <- prabinit(prabmatrix=siskiyou, neighborhood=siskiyou.nb,
              distance="logkulczynski")  
  groupvector <- as.factor(siskiyou.groups)
  ng <- length(levels(groupvector))
  lg <- levels(groupvector)
  nsg <- numeric(0)
    for (i in 1:ng) nsg[i] <- sum(groupvector==lg[i])
  groupinfo <- list(lg=lg,ng=ng,nsg=nsg)
  specgroups(x$distmat,groupvector,groupinfo)

prabclus documentation built on Oct. 24, 2023, 1:06 a.m.