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prabclus (version 2.3-3)

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

13,417

Version

2.3-3

License

GPL

Maintainer

Christian Hennig

Last Published

October 24th, 2023

Functions in prabclus (2.3-3)

Geographical coordinates to distances

Generate spatial weights from prabclus neighborhood list

Compare species clustering and species groups

Construct communities from individuals

Dice distance matrix

Simulation of presence-absence matrices (clustered)

Region-wise cluster membership

Connected regions per species

Connectivity components of an undirected graph

Jaccard distance matrix

Distance ratio test statistics for distance based clustering

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

Distances between communities

Kulczynski distance matrix

Nestedness matrix

Neighborhood list from geographical distance

Classical distance-based test for homogeneity against clustering

Largest connectivity component

Piecewise linear transformation for distance matrices

prab.sarestimate

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

Visualises clusters of markers vs. species

Snail presence-absence data from Aegean sea

Plots for within-groups and between-groups distance regression

p-value simulation for presence-absence matrices clustering test

geco distance matrix

Neighborhood list for Aegean islands

Missing values statistics for matrix

Test of neighborhood list

Mean distance to kth nearest neighbor

prabclus-package

prabclus package overview

Distances between communities, auxiliary functions

Regression between subsets of dissimilarity matrices

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

Presence-absence/abundance matrix initialization

Simulation of presence-absence matrices (non-clustered)

Regression difference between within-group dissimilarities

Quantitative Kulczynski distance matrix

regdistbetweenone

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

Genetic AFLP data of Veronica plants

unbuild.charmatrix

Internal: create allele list out of character matrix

Microsatellite genetic data of Tetragonula bees

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

Parametric bootstrap test for clustering in presence-absence matrices

Herbs of the Siskiyou Mountains

Simulation of abundance matrices (non-clustered)

Average within-group distances for given groups

Regression difference within reference group and between-group dissimilarities

Testing equality of two distance-regressions

Stress values for different dimensions of Kruskal's MDS

Overwater distances between islands in the Aegean sea

Convert abundance matrix into presence/absence matrix

Internal: compares two pairs of alleles

Format conversion for codominant marker data

build.ext.nblist

Internal: generates neighborhood list for diploid loci

Shared allele distance for diploid loci

build.charmatrix

Internal: create character matrix out of allele list

Converts alleleobject into binary matrix

Nearest neighbor based clutter/noise detection

Spatial autocorrelation parameter estimation

Parametric bootstrap test for clustering in abundance matrices

Diploid loci matrix initialization