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prabclus (version 2.2-5)

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

2.2-5

License

GPL

Maintainer

Christian Hennig

Last Published

January 13th, 2015

Functions in prabclus (2.2-5)

Format conversion for codominant marker data

Dice distance matrix

Parametric bootstrap test for clustering in abundance matrices

Nestedness matrix

Nearest neighbor based clutter/noise detection

Diploid loci matrix initialization

Converts alleleobject into binary matrix

build.charmatrix

Internal: create character matrix out of allele list

Test of neighborhood list

Geographical coordinates to distances

Classical distance-based test for homogeneity against clustering

prabclus-package

prabclus package overview

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

geco distance matrix

Simulation of abundance matrices (non-clustered)

Compare species clustering and species groups

Connectivity components of an undirected graph

Connected regions per species

Simulation of presence-absence matrices (clustered)

Overwater distances between islands in the Aegean sea

Microsatellite genetic data of Tetragonula bees

Piecewise linear transformation for distance matrices

Presence-absence/abundance matrix initialization

Herbs of the Siskiyou Mountains

Parametric bootstrap test for clustering in presence-absence matrices

Quantitative Kulczynski distance matrix

Visualises clusters of markers vs. species

p-value simulation for presence-absence matrices clustering test

Neighborhood list for Aegean islands

Average within-group distances for given groups

Largest connectivity component

prab.sarestimate

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

Convert abundance matrix into presence/absence matrix

Stress values for different dimensions of Kruskal's MDS

Kulczynski distance matrix

Internal: compares two pairs of alleles

Region-wise cluster membership

Jaccard distance matrix

build.ext.nblist

Internal: generates neighborhood list for diploid loci

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

Spatial autocorrelation parameter estimation

Genetic AFLP data of Veronica plants

Snail presence-absence data from Aegean sea

Generate spatial weights from prabclus neighborhood list

Mean distance to kth nearest neighbor

unbuild.charmatrix

Internal: create allele list out of character matrix

Simulation of presence-absence matrices (non-clustered)

Shared allele distance for diploid loci

Distance ratio test statistics for distance based clustering

Missing values statistics for matrix

Neighborhood list from geographical distance