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prabclus (version 2.3-4)

Functions for Clustering and Testing 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 genetic data for species delimitation, nearest neighbor based noise detection. Genetic distances between communities. Tests whether various distance-based regressions are equal. Try package?prabclus for on overview.

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Version

Install

install.packages('prabclus')

Monthly Downloads

19,397

Version

2.3-4

License

GPL

Maintainer

Christian Hennig

Last Published

September 24th, 2024

Functions in prabclus (2.3-4)

Diploid loci matrix initialization

build.ext.nblist

Internal: generates neighborhood list for diploid loci

build.charmatrix

Internal: create character matrix out of allele list

Generate spatial weights from prabclus neighborhood list

Simulation of presence-absence matrices (clustered)

Jaccard distance matrix

Compare species clustering and species groups

Parametric bootstrap test for clustering in abundance matrices

Converts alleleobject into binary matrix

Format conversion for codominant marker data

Spatial autocorrelation parameter estimation

Construct communities from individuals

Distances between communities

p-value simulation for presence-absence matrices clustering test

Kulczynski distance matrix

Connectivity components of an undirected graph

Dice distance matrix

Region-wise cluster membership

Nestedness matrix

Visualises clusters of markers vs. species

Missing values statistics for matrix

Connected regions per species

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

Mean distance to kth nearest neighbor

Distances between communities, auxiliary functions

prabclus-package

prabclus package overview

Snail presence-absence data from Aegean sea

Geographical coordinates to distances

Largest connectivity component

Distance ratio test statistics for distance based clustering

Regression between subsets of dissimilarity matrices

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

regdistbetweenone

Testing equality of one within-group and between-two groups distances regression

Test of neighborhood list

prab.sarestimate

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

Presence-absence/abundance matrix initialization

geco distance matrix

Simulation of abundance matrices (non-clustered)

Regression difference between within-group dissimilarities

Herbs of the Siskiyou Mountains

Piecewise linear transformation for distance matrices

Neighborhood list from geographical distance

Classical distance-based test for homogeneity against clustering

Parametric bootstrap test for clustering in presence-absence matrices

Plots for within-groups and between-groups distance regression

Neighborhood list for Aegean islands

Quantitative Kulczynski distance matrix

Microsatellite genetic data of Tetragonula bees

Testing equality of within-groups and between-groups distances regression

Simulation of presence-absence matrices (non-clustered)

Convert abundance matrix into presence/absence matrix

unbuild.charmatrix

Internal: create allele list out of character matrix

Genetic AFLP data of Veronica plants

Average within-group distances for given groups

Stress values for different dimensions of Kruskal's MDS

Overwater distances between islands in the Aegean sea

Regression difference within reference group and between-group dissimilarities

Testing equality of two distance-regressions

Shared allele distance for diploid loci

Nearest neighbor based clutter/noise detection

Internal: compares two pairs of alleles