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prabclus (version 2.3-1)

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 genetical 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

2.3-1

License

GPL

Maintainer

Christian Hennig

Last Published

June 4th, 2019

Functions in prabclus (2.3-1)

build.charmatrix

Internal: create character matrix out of allele list
alleleconvert

Format conversion for codominant marker data
allele2zeroone

Converts alleleobject into binary matrix
alleleinit

Diploid loci matrix initialization
allelepaircomp

Internal: compares two pairs of alleles
build.ext.nblist

Internal: generates neighborhood list for diploid loci
NNclean

Nearest neighbor based clutter/noise detection
autoconst

Spatial autocorrelation parameter estimation
abundtest

Parametric bootstrap test for clustering in abundance matrices
alleledist

Shared allele distance for diploid loci
communitydist

Distances between communities
communities

Construct communities from individuals
build.nblist

Generate spatial weights from prabclus neighborhood list
jaccard

Jaccard distance matrix
cluspop.nb

Simulation of presence-absence matrices (clustered)
nbtest

Test of neighborhood list
nb

Neighborhood list for Aegean islands
homogen.test

Classical distance-based test for homogeneity against clustering
geo2neighbor

Neighborhood list from geographical distance
crmatrix

Region-wise cluster membership
comp.test

Compare species clustering and species groups
nn

Mean distance to kth nearest neighbor
kulczynski

Kulczynski distance matrix
con.comp

Connectivity components of an undirected graph
dicedist

Dice distance matrix
phipt

Distances between communities, auxiliary functions
prabinit

Presence-absence/abundance matrix initialization
prabtest

Parametric bootstrap test for clustering in presence-absence matrices
lcomponent

Largest connectivity component
lociplots

Visualises clusters of markers vs. species
kykladspecreg

Snail presence-absence data from Aegean sea
nastats

Missing values statistics for matrix
geco

geco distance matrix
distratio

Distance ratio test statistics for distance based clustering
pop.sim

p-value simulation for presence-absence matrices clustering test
regdistbetweenone

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

Simulation of presence-absence matrices (non-clustered)
qkulczynski

Quantitative Kulczynski distance matrix
unbuild.charmatrix

Internal: create allele list out of character matrix
veronica

Genetic AFLP data of Veronica plants
coord2dist

Geographical coordinates to distances
con.regmat

Connected regions per species
specgroups

Average within-group distances for given groups
regdistdiff

Regression difference between within-group dissimilarities
tetragonula

Microsatellite genetic data of Tetragonula bees
waterdist

Overwater distances between islands in the Aegean sea
toprab

Convert abundance matrix into presence/absence matrix
stressvals

Stress values for different dimensions of Kruskal's MDS
piecewiselin

Piecewise linear transformation for distance matrices
hprabclust

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

Plots for within-groups and between-groups distance regression
incmatrix

Nestedness matrix
prabclust

Clustering for biotic elements or for species delimitation (mixture method)
prabclus-package

prabclus package overview
regdistdiffone

Regression difference within reference group and between-group dissimilarities
regdist

Regression between subsets of dissimilarity matrices
prab.sarestimate

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

Testing equality of two distance-regressions
siskiyou

Herbs of the Siskiyou Mountains
regdistbetween

Testing equality of within-groups and between-groups distances regression
regpop.sar

Simulation of abundance matrices (non-clustered)