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prabclus (version 2.3-2)

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

2.3-2

License

GPL

Maintainer

Christian Hennig

Last Published

January 8th, 2020

Functions in prabclus (2.3-2)

Converts alleleobject into binary matrix

Snail presence-absence data from Aegean sea

Construct communities from individuals

Internal: compares two pairs of alleles

Nestedness matrix

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

Distances between communities

Spatial autocorrelation parameter estimation

Piecewise linear transformation for distance matrices

Plots for within-groups and between-groups distance regression

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

Regression between subsets of dissimilarity matrices

Testing equality of two distance-regressions

Largest connectivity component

Regression difference within reference group and between-group dissimilarities

Classical distance-based test for homogeneity against clustering

prab.sarestimate

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

p-value simulation for presence-absence matrices clustering test

Neighborhood list from geographical distance

prabclus-package

prabclus package overview

Visualises clusters of markers vs. species

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

Presence-absence/abundance matrix initialization

Missing values statistics for matrix

Diploid loci matrix initialization

Average within-group distances for given groups

Shared allele distance for diploid loci

Generate spatial weights from prabclus neighborhood list

Parametric bootstrap test for clustering in presence-absence matrices

Jaccard distance matrix

Simulation of presence-absence matrices (clustered)

Kulczynski distance matrix

Overwater distances between islands in the Aegean sea

Stress values for different dimensions of Kruskal's MDS

Convert abundance matrix into presence/absence matrix

Microsatellite genetic data of Tetragonula bees

Nearest neighbor based clutter/noise detection

Parametric bootstrap test for clustering in abundance matrices

Connected regions per species

Distances between communities, auxiliary functions

Mean distance to kth nearest neighbor

Simulation of presence-absence matrices (non-clustered)

Quantitative Kulczynski distance matrix

Geographical coordinates to distances

Simulation of abundance matrices (non-clustered)

Herbs of the Siskiyou Mountains

Distance ratio test statistics for distance based clustering

geco distance matrix

Test of neighborhood list

regdistbetweenone

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

Neighborhood list for Aegean islands

Genetic AFLP data of Veronica plants

unbuild.charmatrix

Internal: create allele list out of character matrix

Regression difference between within-group dissimilarities

build.charmatrix

Internal: create character matrix out of allele list

build.ext.nblist

Internal: generates neighborhood list for diploid loci

Format conversion for codominant marker data

Compare species clustering and species groups

Connectivity components of an undirected graph

Dice distance matrix

Region-wise cluster membership