prabclus: Functions for Clustering of Presence-Absence, Abundance and Multilocus Genetic Data
Version 2.2-6

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
URL http://www.homepages.ucl.ac.uk/~ucakche
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("prabclus")

Getting started

Package overview

Popular man pages

dicedist: Dice distance matrix
jaccard: Jaccard distance matrix
kulczynski: Kulczynski distance matrix
nb: Neighborhood list for Aegean islands
pop.sim: p-value simulation for presence-absence matrices clustering...
tetragonula: Microsatellite genetic data of Tetragonula bees
toprab: Convert abundance matrix into presence/absence matrix
See all...

All man pages Function index File listing

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

Functions

NNclean Man page Source code
abundtest Man page Source code
allele2zeroone Man page Source code
alleleconvert Man page Source code
alleledist Man page Source code
alleleinit Man page Source code
alleleobject Man page
allelepaircomp Man page Source code
autoconst Man page Source code
autoreg Man page Source code
build.charmatrix Man page Source code
build.ext.nblist Man page Source code
build.nblist Man page Source code
cluspop.nb Man page
comp.test Man page Source code
con.comp Man page
con.regmat Man page Source code
coord2dist Man page Source code
crmatrix Man page Source code
dicedist Man page Source code
distratio Man page
geco Man page Source code
geo2neighbor Man page Source code
homogen.test Man page
hprabclust Man page Source code
incmatrix Man page
jaccard Man page
kulczynski Man page
kykladspecreg Man page
lcomponent Man page
lociplots Man page Source code
nastats Man page Source code
nb Man page
nbtest Man page
nn Man page
piecewiselin Man page Source code
pop.sim Man page Source code
prab Man page
prab.sarestimate Man page Source code
prabclus-package Man page
prabclust Man page Source code
prabinit Man page Source code
prabtest Man page Source code
print.alleleobject Man page Source code
print.comprabclust Man page
print.nnclean Man page Source code
print.prab Man page
print.prabclust Man page
print.summary.prabtest Man page
qkulczynski Man page Source code
randpop.nb Man page
regpop.sar Man page Source code
siskiyou Man page
siskiyou.groups Man page
siskiyou.nb Man page
specgroups Man page Source code
stressvals Man page Source code
summary.prabtest Man page
tetragonula Man page
tetragonula.coord Man page
toprab Man page Source code
unbuild.charmatrix Man page Source code
veronica Man page
veronica.coord Man page
waterdist Man page

Files

inst
inst/extdata
inst/extdata/LeiMik1NB.txt
inst/extdata/Franck04koord.txt
inst/extdata/Heterotrigona_indoFO.txt
inst/extdata/00Index.old
inst/extdata/nb.R
inst/extdata/MartinezOrtega04AFLP.txt
inst/extdata/veronica.R
inst/extdata/tetragonula.R
inst/extdata/nb.txt
inst/extdata/MartinezKoord.txt
inst/extdata/LeiMik1G.txt
inst/extdata/LeiMik1.txt
inst/extdata/siskiyou.R
tests
tests/donttestexamples.R
tests/Examples
tests/Examples/prabclus-Ex.Rout.save
tests/prabclustests.R
tests/prabclustests.Rout.save
NAMESPACE
data
data/waterdist.rda
data/nb.rda
data/veronica.rda
data/siskiyou.rda
data/kykladspecreg.txt.gz
data/waterdist.txt.gz
data/kykladspecreg.rda
data/tetragonula.rda
R
R/kulczynski.R
R/geodist.R
R/homogen.test.R
R/alleletest.R
R/NNclean.R
R/comp.test.R
R/autoreg.R
R/jaccard.R
R/pop.sim.R
R/distratio.R
R/print.prabclust.R
R/lcomponent.R
R/prabclust.R
R/print.prab.R
R/prabinit.R
R/newprabmatrix.R
R/qkulczynski.R
R/nbtest.R
R/nn.R
R/randpop.nb.R
R/conregmat.R
R/concomp.R
R/cluspop.nb.R
R/incmatrix.R
R/abundfunctions.R
MD5
README
DESCRIPTION
man
man/cluspop.nb.Rd
man/conregmat.Rd
man/lcomponent.Rd
man/lociplots.Rd
man/coord2dist.Rd
man/crmatrix.Rd
man/hprabclust.Rd
man/siskiyou.Rd
man/build.ext.nblist.Rd
man/autoconst.Rd
man/prabinit.Rd
man/pop.sim.Rd
man/waterdist.Rd
man/dicedist.Rd
man/tetragonula.Rd
man/nb.Rd
man/piecewiselin.Rd
man/concomp.Rd
man/alleleconvert.Rd
man/kulczynski.Rd
man/kykladspecreg.Rd
man/homogen.test.Rd
man/prabclus-package.Rd
man/alleleinit.Rd
man/toprab.Rd
man/distratio.Rd
man/allelepaircomp.Rd
man/alleledist.Rd
man/incmatrix.Rd
man/geo2neighbor.Rd
man/build.nblist.Rd
man/unbuild.charmatrix.Rd
man/geco.Rd
man/jaccard.Rd
man/prabtest.Rd
man/stressvals.Rd
man/nn.Rd
man/randpop.nb.Rd
man/comp.test.Rd
man/nbtest.Rd
man/abundtest.Rd
man/specgroups.Rd
man/build.charmatrix.Rd
man/prab.sarestimate.Rd
man/nastats.Rd
man/prabclust.Rd
man/regpop.sar.Rd
man/veronica.Rd
man/allele2zeroone.Rd
man/NNclean.Rd
man/qkulczynski.Rd
prabclus documentation built on May 19, 2017, 6:23 p.m.