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prabclus (version 2.2-7)

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

16,866

Version

2.2-7

License

GPL

Maintainer

Christian Hennig

Last Published

January 17th, 2019

Functions in prabclus (2.2-7)

geco distance matrix

Visualises clusters of markers vs. species

Largest connectivity component

Missing values statistics for matrix

Converts alleleobject into binary matrix

Presence-absence/abundance matrix initialization

Format conversion for codominant marker data

Internal: compares two pairs of alleles

Region-wise cluster membership

Spatial autocorrelation parameter estimation

Dice distance matrix

Compare species clustering and species groups

Connectivity components of an undirected graph

Neighborhood list from geographical distance

Neighborhood list for Aegean islands

Classical distance-based test for homogeneity against clustering

prabclus-package

prabclus package overview

Quantitative Kulczynski distance matrix

Test of neighborhood list

Simulation of abundance matrices (non-clustered)

Overwater distances between islands in the Aegean sea

Parametric bootstrap test for clustering in presence-absence matrices

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

Simulation of presence-absence matrices (non-clustered)

Microsatellite genetic data of Tetragonula bees

Herbs of the Siskiyou Mountains

build.charmatrix

Internal: create character matrix out of allele list

Convert abundance matrix into presence/absence matrix

build.ext.nblist

Internal: generates neighborhood list for diploid loci

Connected regions per species

Geographical coordinates to distances

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

Nestedness matrix

Mean distance to kth nearest neighbor

Piecewise linear transformation for distance matrices

Shared allele distance for diploid loci

unbuild.charmatrix

Internal: create allele list out of character matrix

Diploid loci matrix initialization

Generate spatial weights from prabclus neighborhood list

Simulation of presence-absence matrices (clustered)

Genetic AFLP data of Veronica plants

Kulczynski distance matrix

Jaccard distance matrix

p-value simulation for presence-absence matrices clustering test

prab.sarestimate

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

Average within-group distances for given groups

Stress values for different dimensions of Kruskal's MDS

Snail presence-absence data from Aegean sea

Nearest neighbor based clutter/noise detection

Distance ratio test statistics for distance based clustering

Parametric bootstrap test for clustering in abundance matrices