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prabclus (version 2.2-4)

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.

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Version

Install

install.packages('prabclus')

Monthly Downloads

20,025

Version

2.2-4

License

GPL

Maintainer

Christian Hennig

Last Published

August 25th, 2012

Functions in prabclus (2.2-4)

Spatial autocorrelation parameter estimation

Shared allele distance for diploid loci

build.ext.nblist

Internal: generates neighborhood list for diploid loci

Parametric bootstrap test for clustering in abundance matrices

Neighborhood list for Aegean islands

Distance ratio test statistics for distance based clustering

Average within-group distances for given groups

build.charmatrix

Internal: create character matrix out of allele list

Simulation of presence-absence matrices (clustered)

Geographical coordinates to distances

prab.sarestimate

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

Genetic AFLP data of Veronica plants

Neighborhood list from geographical distance

Visualises clusters of markers vs. species

Compare species clustering and species groups

Mean distance to kth nearest neighbor

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

geco distance matrix

Convert abundance matrix into presence/absence matrix

Stress values for different dimensions of Kruskal's MDS

prabclus-package

prabclus package overview

Snail presence-absence data from Aegean sea

Connectivity components of an undirected graph

Region-wise cluster membership

Parametric bootstrap test for clustering in presence-absence matrices

Microsatellite genetic data of Tetragonula bees

Classical distance-based test for homogeneity against clustering

Largest connectivity component

Nestedness matrix

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

Overwater distances between islands in the Aegean sea

Simulation of abundance matrices (non-clustered)

Nearest neighbor based clutter/noise detection

Format conversion for codominant marker data

Test of neighborhood list

Jaccard distance matrix

Dice distance matrix

Kulczynski distance matrix

Quantitative Kulczynski distance matrix

Presence-absence/abundance matrix initialization

unbuild.charmatrix

Internal: create allele list out of character matrix

Piecewise linear transformation for distance matrices

p-value simulation for presence-absence matrices clustering test

Herbs of the Siskiyou Mountains

Converts alleleobject into binary matrix

Generate spatial weights from prabclus neighborhood list

Simulation of presence-absence matrices (non-clustered)

Connected regions per species

Missing values statistics for matrix

Internal: compares two pairs of alleles

Diploid loci matrix initialization