Package: prabclus 2.3-3

prabclus: Functions for Clustering and Testing 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 genetic data for species delimitation, nearest neighbor based noise detection. Genetic distances between communities. Tests whether various distance-based regressions are equal. Try package?prabclus for on overview.

Authors:Christian Hennig <[email protected]>, Bernhard Hausdorf <[email protected]>

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prabclus.pdf |prabclus.html✨
prabclus/json (API)

# Install 'prabclus' in R:
install.packages('prabclus', repos = c('https://chrhennig.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

67 exports 1 stars 5.51 score 2 dependencies 69 dependents 4 mentions 79 scripts 10.3k downloads

Last updated 11 months agofrom:dfb0e5ea96. Checks:OK: 5 NOTE: 2. Indexed: yes.

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Doc / VignettesOKAug 20 2024
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R-4.4-winOKAug 20 2024
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R-4.3-macOKAug 20 2024

Exports:abundtestallele2zeroonealleleconvertalleledistalleleinitallelepaircompautoconstautoregbuild.charmatrixbuild.ext.nblistbuild.nblistcfchordcluspop.nbcommunitiescommunitydistcomp.testcon.compcon.regmatcoord2distcrmatrixdicedistdiploidcomlistdistratiogecogeo2neighborhomogen.testhprabclustincmatrixjaccardkulczynskilcomponentlociplotsnastatsnbtestnnNNcleanphiptpiecewiselinplotdistregpop.simprab.sarestimateprabclustprabinitprabtestprint.alleleobjectprint.comprabclustprint.nncleanprint.prabprint.prabclustprint.regdistbetweenprint.regeqdistprint.summary.prabtestqkulczynskirandpop.nbregdistregdistbetweenregdistbetweenoneregdistdiffregdistdiffoneregeqdistregpop.sarshared.problistspecgroupsstressvalssummary.prabtesttoprabunbuild.charmatrix

Dependencies:MASSmclust

Readme and manuals

Help Manual

Help pageTopics
prabclus package overviewprabclus-package
Parametric bootstrap test for clustering in abundance matricesabundtest
Converts alleleobject into binary matrixallele2zeroone
Format conversion for codominant marker dataalleleconvert
Shared allele distance for diploid locialleledist
Diploid loci matrix initializationalleleinit alleleobject print.alleleobject
Internal: compares two pairs of allelesallelepaircomp
Spatial autocorrelation parameter estimationautoconst autoreg
Internal: create character matrix out of allele listbuild.charmatrix
Internal: generates neighborhood list for diploid locibuild.ext.nblist
Generate spatial weights from prabclus neighborhood listbuild.nblist
Simulation of presence-absence matrices (clustered)cluspop.nb
Construct communities from individualscommunities
Distances between communitiescommunitydist
Compare species clustering and species groupscomp.test
Connectivity components of an undirected graphcon.comp
Connected regions per speciescon.regmat
Geographical coordinates to distancescoord2dist
Region-wise cluster membershipcrmatrix
Dice distance matrixdicedist
Distance ratio test statistics for distance based clusteringdistratio
geco distance matrixgeco
Neighborhood list from geographical distancegeo2neighbor
Classical distance-based test for homogeneity against clusteringhomogen.test
Clustering of species ranges from presence-absence matrices (hierarchical methods)hprabclust print.comprabclust
Nestedness matrixincmatrix
Jaccard distance matrixjaccard
Kulczynski distance matrixkulczynski
Snail presence-absence data from Aegean seakykladspecreg
Largest connectivity componentlcomponent
Visualises clusters of markers vs. specieslociplots
Missing values statistics for matrixnastats
Neighborhood list for Aegean islandsnb
Test of neighborhood listnbtest
Mean distance to kth nearest neighbornn
Nearest neighbor based clutter/noise detectionNNclean print.nnclean
Distances between communities, auxiliary functionscfchord diploidcomlist phipt shared.problist
Piecewise linear transformation for distance matricespiecewiselin
Plots for within-groups and between-groups distance regressionplotdistreg
p-value simulation for presence-absence matrices clustering testpop.sim
Estimates SAR model from log-abundance matrix of prab-object.prab.sarestimate
Clustering for biotic elements or for species delimitation (mixture method)prabclust print.prabclust
Presence-absence/abundance matrix initializationprab prabinit print.prab
Parametric bootstrap test for clustering in presence-absence matricesprabtest print.summary.prabtest summary.prabtest
Quantitative Kulczynski distance matrixqkulczynski
Simulation of presence-absence matrices (non-clustered)randpop.nb
Regression between subsets of dissimilarity matricesregdist
Testing equality of within-groups and between-groups distances regressionprint.regdistbetween regdistbetween
Testing equality of one within-group and between-two groups distances regressionregdistbetweenone
Regression difference between within-group dissimilaritiesregdistdiff
Regression difference within reference group and between-group dissimilaritiesregdistdiffone
Testing equality of two distance-regressionsprint.regeqdist regeqdist
Simulation of abundance matrices (non-clustered)regpop.sar
Herbs of the Siskiyou Mountainssiskiyou siskiyou.groups siskiyou.nb
Average within-group distances for given groupsspecgroups
Stress values for different dimensions of Kruskal's MDSstressvals
Microsatellite genetic data of Tetragonula beestetragonula tetragonula.coord
Convert abundance matrix into presence/absence matrixtoprab
Internal: create allele list out of character matrixunbuild.charmatrix
Genetic AFLP data of Veronica plantsveronica veronica.coord
Overwater distances between islands in the Aegean seawaterdist