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prabclus (version 2.2-2)

Functions for clustering of presence-absence, abundance and multilocus genetic data

Description

Distance-based parametric bootstrap tests for clustering with spatial neighborhood information. Some distance measures, Clustering of presence-absence, abundance and multilocus genetical data for species delimitation, nearest neighbor based noise detection. Try package?prabclus for on overview. Note that the use of the package mclust (called by function prabclust) is protected by a special license, see http://www.stat.washington.edu/mclust/license.txt, particularly point 6.

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Version

Install

install.packages('prabclus')

Monthly Downloads

20,025

Version

2.2-2

License

GPL

Maintainer

Christian Hennig

Last Published

September 16th, 2010

Functions in prabclus (2.2-2)

NNclean

Nearest neighbor based clutter/noise detection
alleleconvert

Format conversion for codominant marker data
build.charmatrix

Internal: create character matrix out of allele list
build.ext.nblist

Internal: generates neighborhood list for diploid loci
allelepaircomp

Internal: compares two pairs of alleles
lcomponent

Largest connectivity component
lociplots

Visualises clusters of markers vs. species
nbtest

Test of neighborhood list
con.comp

Connectivity components of an undirected graph
prabinit

Presence-absence/abundance matrix initialization
jaccard

Jaccard distance matrix
dicedist

Dice distance matrix
comp.test

Compare species clustering and species groups
unbuild.charmatrix

Internal: create allele list out of character matrix
kykladspecreg

Snail presence-absence data from Aegean sea
con.regmat

Connected regions per species
alleleinit

Diploid loci matrix initialization
pop.sim

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

Overwater distances between islands in the Aegean sea
specgroups

Average within-group distances for given groups
kulczynski

Kulczynski distance matrix
nn

Mean distance to kth nearest neighbor
incmatrix

Nestedness matrix
hprabclust

Clustering of species ranges from presence-absence matrices (hierarchical methods)
toprab

Convert abundance matrix into presence/absence matrix
tetragonula

Microsatellite genetic data of Tetragonula bees
autoconst

Spatial autocorrelation parameter estimation
geo2neighbor

Neighborhood list from geographical distance
geco

geco distance matrix
coord2dist

Geographical coordinates to distances
prabclust

Clustering for biotic elements or for species delimitation (mixture method)
abundtest

Parametric bootstrap test for clustering in abundance matrices
homogen.test

Classical distance-based test for homogeneity against clustering
allele2zeroone

Converts alleleobject into binary matrix
distratio

Distance ratio test statistics for distance based clustering
prab.sarestimate

Estimates SAR model from log-abundance matrix of prab-object.
stressvals

Stress values for different dimensions of Kruskal's MDS
nb

Neighborhood list for Aegean islands
piecewiselin

Piecewise linear transformation for distance matrices
veronica

Genetic AFLP data of Veronica plants
qkulczynski

Quantitative Kulczynski distance matrix
nastats

Missing values statistics for matrix
randpop.nb

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

Herbs of the Siskiyou Mountains
regpop.sar

Simulation of abundance matrices (non-clustered)
prabtest

Parametric bootstrap test for clustering in presence-absence matrices
alleledist

Shared allele distance for diploid loci
cluspop.nb

Simulation of presence-absence matrices (clustered)
build.nblist

Generate spatial weights from prabclus neighborhood list
prabclus-package

prabclus package overview