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prabclus (version 1.0-1)

Test for clustering of presence-absence data

Description

Distance based parametric bootstrap tests for clustering, mainly thought for presence-absence data (clustering of species distribution maps). Jaccard and Kulczynski distance measures, clustering of MDS scores, and nearest neighbor based noise detection (R port of Byers and Raftery's (1998) "NNclean"). Main functions are prabtest (for testing), prabclust (for clustering), prabinit (for preparing the data) and NNclean (for noise detection). The help-pages for prabtest and prabclust contain simple standard executions.

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Version

Install

install.packages('prabclus')

Monthly Downloads

20,025

Version

1.0-1

License

GPL

Maintainer

Christian Hennig

Last Published

September 24th, 2024

Functions in prabclus (1.0-1)

prabclust

Clustering of species ranges from presence-absence matrices
distratio

Distance ratio test statistics for distance based clustering
nb

Neighborhood list for Aegean islands
prabtest

Parametric bootstrap test for clustering in presence-absence matrices
jaccard

Jaccard distance matrix
autoconst

Spatial autocorrelation parameter estimation
prabinit

Presence-absence matrix initialization
kulczynski

Kulczynski distance matrix
randpop.nb

Simulation of presence-absence matrices (non-clustered)
cluspop.nb

Simulation of presence-absence matrices (clustered)
nn

Mean distance to kth nearest neighbor
con.regmat

Connected regions per species
nbtest

Test of neighborhood list
pop.sim

p-value simulation for presence-absence matrices clustering test
incmatrix

Nestedness matrix
kykladspecreg

Snail presence-absence data from Aegean sea
con.comp

Connectivity components of an undirected graph
comp.test

Compare species clustering and species groups
homogen.test

Classical distance-based test for homogeneity against clustering
lcomponent

Largest connectivity component
NNclean

Nearest neighbor based clutter/noise detection
summary.prabtest

Print and summary method for prabtest