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

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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
URLs

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