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prabclus (version 2.2-6)

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

2.2-6

License

GPL

Maintainer

Christian Hennig

Last Published

January 14th, 2015

Functions in prabclus (2.2-6)

Herbs of the Siskiyou Mountains

Overwater distances between islands in the Aegean sea

Largest connectivity component

unbuild.charmatrix

Internal: create allele list out of character matrix

Diploid loci matrix initialization

Parametric bootstrap test for clustering in abundance matrices

Internal: compares two pairs of alleles

Jaccard distance matrix

Simulation of presence-absence matrices (non-clustered)

Simulation of abundance matrices (non-clustered)

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

Convert abundance matrix into presence/absence matrix

Converts alleleobject into binary matrix

Connectivity components of an undirected graph

Region-wise cluster membership

Spatial autocorrelation parameter estimation

build.charmatrix

Internal: create character matrix out of allele list

Geographical coordinates to distances

Microsatellite genetic data of Tetragonula bees

Parametric bootstrap test for clustering in presence-absence matrices

Simulation of presence-absence matrices (clustered)

Average within-group distances for given groups

build.ext.nblist

Internal: generates neighborhood list for diploid loci

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

Connected regions per species

Neighborhood list from geographical distance

Visualises clusters of markers vs. species

Nestedness matrix

Classical distance-based test for homogeneity against clustering

Nearest neighbor based clutter/noise detection

Quantitative Kulczynski distance matrix

Neighborhood list for Aegean islands

geco distance matrix

Distance ratio test statistics for distance based clustering

Kulczynski distance matrix

Presence-absence/abundance matrix initialization

Shared allele distance for diploid loci

Mean distance to kth nearest neighbor

Stress values for different dimensions of Kruskal's MDS

prab.sarestimate

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

Format conversion for codominant marker data

Compare species clustering and species groups

Missing values statistics for matrix

Generate spatial weights from prabclus neighborhood list

prabclus-package

prabclus package overview

p-value simulation for presence-absence matrices clustering test

Genetic AFLP data of Veronica plants

Dice distance matrix

Snail presence-absence data from Aegean sea

Test of neighborhood list

Piecewise linear transformation for distance matrices