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prabclus (version 2.0-1)

Test for clustering of presence-absence data

Description

Distance-based parametric bootstrap tests for clustering, mainly intended for presence-absence data (clustering of species distribution maps). Jaccard, Kulczynski and geco distance measures, clustering of presence-absence and abundance data, 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

2.0-1

License

GPL

Maintainer

Christian Hennig

Last Published

September 24th, 2024

Functions in prabclus (2.0-1)

con.comp

Connectivity components of an undirected graph
incmatrix

Nestedness matrix
distratio

Distance ratio test statistics for distance based clustering
nn

Mean distance to kth nearest neighbor
summary.prabtest

Print and summary method for prabtest
geco

geco distance matrix
jaccard

Jaccard distance matrix
prabclust

Clustering of species ranges from presence-absence matrices (mixture method)
pop.sim

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

Clustering of species ranges from presence-absence matrices (hierarchical methods)
randpop.nb

Simulation of presence-absence matrices (non-clustered)
NNclean

Nearest neighbor based clutter/noise detection
homogen.test

Classical distance-based test for homogeneity against clustering
prabtest

Parametric bootstrap test for clustering in presence-absence matrices
lcomponent

Largest connectivity component
geo2neighbor

Neighborhood list from geographical distance
nb

Neighborhood list for Aegean islands
nbtest

Test of neighborhood list
autoconst

Spatial autocorrelation parameter estimation
waterdist

Overwater distances between islands in the Aegean sea
con.regmat

Connected regions per species
comp.test

Compare species clustering and species groups
cluspop.nb

Simulation of presence-absence matrices (clustered)
prabinit

Presence-absence/abundance matrix initialization
qkulczynski

Quantitative Kulczynski distance matrix
kykladspecreg

Snail presence-absence data from Aegean sea
piecewiselin

Piecewise linear transformation for distance matrices
kulczynski

Kulczynski distance matrix