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.

Install the latest version of this package by entering the following in R:
install.packages("prabclus")
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

Functions

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

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

Please suggest features or report bugs with the GitHub issue tracker.

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