prabclus: Functions for Clustering of Presence-Absence, Abundance and Multilocus Genetic Data

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.

AuthorChristian Hennig <c.hennig@ucl.ac.uk>, Bernhard Hausdorf <Hausdorf@zoologie.uni-hamburg.de>
Date of publication2015-01-14 22:49:24
MaintainerChristian Hennig <c.hennig@ucl.ac.uk>
LicenseGPL
Version2.2-6
http://www.homepages.ucl.ac.uk/~ucakche

View on CRAN

Man pages

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

Files in this package

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.