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.

Author | Christian Hennig <c.hennig@ucl.ac.uk>, Bernhard Hausdorf <Hausdorf@zoologie.uni-hamburg.de> |

Date of publication | 2015-01-14 22:49:24 |

Maintainer | Christian Hennig <c.hennig@ucl.ac.uk> |

License | GPL |

Version | 2.2-6 |

http://www.homepages.ucl.ac.uk/~ucakche |

**abundtest:** Parametric bootstrap test for clustering in abundance...

**allele2zeroone:** Converts alleleobject into binary matrix

**alleleconvert:** Format conversion for codominant marker data

**alleledist:** Shared allele distance for diploid loci

**alleleinit:** Diploid loci matrix initialization

**allelepaircomp:** Internal: compares two pairs of alleles

**autoconst:** Spatial autocorrelation parameter estimation

**build.charmatrix:** Internal: create character matrix out of allele list

**build.ext.nblist:** Internal: generates neighborhood list for diploid loci

**build.nblist:** Generate spatial weights from prabclus neighborhood list

**cluspop.nb:** Simulation of presence-absence matrices (clustered)

**comp.test:** Compare species clustering and species groups

**concomp:** Connectivity components of an undirected graph

**conregmat:** Connected regions per species

**coord2dist:** Geographical coordinates to distances

**crmatrix:** Region-wise cluster membership

**dicedist:** Dice distance matrix

**distratio:** Distance ratio test statistics for distance based clustering

**geco:** geco distance matrix

**geo2neighbor:** Neighborhood list from geographical distance

**homogen.test:** Classical distance-based test for homogeneity against...

**hprabclust:** Clustering of species ranges from presence-absence matrices...

**incmatrix:** Nestedness matrix

**jaccard:** Jaccard distance matrix

**kulczynski:** Kulczynski distance matrix

**kykladspecreg:** Snail presence-absence data from Aegean sea

**lcomponent:** Largest connectivity component

**lociplots:** Visualises clusters of markers vs. species

**nastats:** Missing values statistics for matrix

**nb:** Neighborhood list for Aegean islands

**nbtest:** Test of neighborhood list

**nn:** Mean distance to kth nearest neighbor

**NNclean:** Nearest neighbor based clutter/noise detection

**piecewiselin:** Piecewise linear transformation for distance matrices

**pop.sim:** p-value simulation for presence-absence matrices clustering...

**prabclus-package:** prabclus package overview

**prabclust:** Clustering for biotic elements or for species delimitation...

**prabinit:** Presence-absence/abundance matrix initialization

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

**prabtest:** Parametric bootstrap test for clustering in presence-absence...

**qkulczynski:** Quantitative Kulczynski distance matrix

**randpop.nb:** Simulation of presence-absence matrices (non-clustered)

**regpop.sar:** Simulation of abundance matrices (non-clustered)

**siskiyou:** Herbs of the Siskiyou Mountains

**specgroups:** Average within-group distances for given groups

**stressvals:** Stress values for different dimensions of Kruskal's MDS

**tetragonula:** Microsatellite genetic data of Tetragonula bees

**toprab:** Convert abundance matrix into presence/absence matrix

**unbuild.charmatrix:** Internal: create allele list out of character matrix

**veronica:** Genetic AFLP data of Veronica plants

**waterdist:** Overwater distances between islands in the Aegean sea

prabclus

prabclus/inst

prabclus/inst/extdata

prabclus/inst/extdata/LeiMik1NB.txt

prabclus/inst/extdata/Franck04koord.txt

prabclus/inst/extdata/Heterotrigona_indoFO.txt

prabclus/inst/extdata/00Index.old

prabclus/inst/extdata/nb.R

prabclus/inst/extdata/MartinezOrtega04AFLP.txt

prabclus/inst/extdata/veronica.R

prabclus/inst/extdata/tetragonula.R

prabclus/inst/extdata/nb.txt

prabclus/inst/extdata/MartinezKoord.txt

prabclus/inst/extdata/LeiMik1G.txt

prabclus/inst/extdata/LeiMik1.txt

prabclus/inst/extdata/siskiyou.R

prabclus/tests

prabclus/tests/donttestexamples.R

prabclus/tests/Examples

prabclus/tests/Examples/prabclus-Ex.Rout.save

prabclus/tests/prabclustests.R

prabclus/tests/prabclustests.Rout.save

prabclus/NAMESPACE

prabclus/data

prabclus/data/waterdist.rda

prabclus/data/nb.rda

prabclus/data/veronica.rda

prabclus/data/siskiyou.rda

prabclus/data/kykladspecreg.txt.gz

prabclus/data/waterdist.txt.gz

prabclus/data/kykladspecreg.rda

prabclus/data/tetragonula.rda

prabclus/R

prabclus/R/kulczynski.R
prabclus/R/geodist.R
prabclus/R/homogen.test.R
prabclus/R/alleletest.R
prabclus/R/NNclean.R
prabclus/R/comp.test.R
prabclus/R/autoreg.R
prabclus/R/jaccard.R
prabclus/R/pop.sim.R
prabclus/R/distratio.R
prabclus/R/print.prabclust.R
prabclus/R/lcomponent.R
prabclus/R/prabclust.R
prabclus/R/print.prab.R
prabclus/R/prabinit.R
prabclus/R/newprabmatrix.R
prabclus/R/qkulczynski.R
prabclus/R/nbtest.R
prabclus/R/nn.R
prabclus/R/randpop.nb.R
prabclus/R/conregmat.R
prabclus/R/concomp.R
prabclus/R/cluspop.nb.R
prabclus/R/incmatrix.R
prabclus/R/abundfunctions.R
prabclus/MD5

prabclus/README

prabclus/DESCRIPTION

prabclus/man

prabclus/man/cluspop.nb.Rd
prabclus/man/conregmat.Rd
prabclus/man/lcomponent.Rd
prabclus/man/lociplots.Rd
prabclus/man/coord2dist.Rd
prabclus/man/crmatrix.Rd
prabclus/man/hprabclust.Rd
prabclus/man/siskiyou.Rd
prabclus/man/build.ext.nblist.Rd
prabclus/man/autoconst.Rd
prabclus/man/prabinit.Rd
prabclus/man/pop.sim.Rd
prabclus/man/waterdist.Rd
prabclus/man/dicedist.Rd
prabclus/man/tetragonula.Rd
prabclus/man/nb.Rd
prabclus/man/piecewiselin.Rd
prabclus/man/concomp.Rd
prabclus/man/alleleconvert.Rd
prabclus/man/kulczynski.Rd
prabclus/man/kykladspecreg.Rd
prabclus/man/homogen.test.Rd
prabclus/man/prabclus-package.Rd
prabclus/man/alleleinit.Rd
prabclus/man/toprab.Rd
prabclus/man/distratio.Rd
prabclus/man/allelepaircomp.Rd
prabclus/man/alleledist.Rd
prabclus/man/incmatrix.Rd
prabclus/man/geo2neighbor.Rd
prabclus/man/build.nblist.Rd
prabclus/man/unbuild.charmatrix.Rd
prabclus/man/geco.Rd
prabclus/man/jaccard.Rd
prabclus/man/prabtest.Rd
prabclus/man/stressvals.Rd
prabclus/man/nn.Rd
prabclus/man/randpop.nb.Rd
prabclus/man/comp.test.Rd
prabclus/man/nbtest.Rd
prabclus/man/abundtest.Rd
prabclus/man/specgroups.Rd
prabclus/man/build.charmatrix.Rd
prabclus/man/prab.sarestimate.Rd
prabclus/man/nastats.Rd
prabclus/man/prabclust.Rd
prabclus/man/regpop.sar.Rd
prabclus/man/veronica.Rd
prabclus/man/allele2zeroone.Rd
prabclus/man/NNclean.Rd
prabclus/man/qkulczynski.Rd
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