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install.packages('prabclus')
Monthly Downloads
97,810
Version
2.3-2
License
GPL
Maintainer
Christian Hennig
Last Published
January 8th, 2020
Functions in prabclus (2.3-2)
Search functions
allele2zeroone
Converts alleleobject into binary matrix
kykladspecreg
Snail presence-absence data from Aegean sea
communities
Construct communities from individuals
allelepaircomp
Internal: compares two pairs of alleles
incmatrix
Nestedness matrix
hprabclust
Clustering of species ranges from presence-absence matrices (hierarchical methods)
communitydist
Distances between communities
autoconst
Spatial autocorrelation parameter estimation
piecewiselin
Piecewise linear transformation for distance matrices
plotdistreg
Plots for within-groups and between-groups distance regression
regdistbetween
Testing equality of within-groups and between-groups distances regression
regdist
Regression between subsets of dissimilarity matrices
regeqdist
Testing equality of two distance-regressions
lcomponent
Largest connectivity component
regdistdiffone
Regression difference within reference group and between-group dissimilarities
homogen.test
Classical distance-based test for homogeneity against clustering
prab.sarestimate
Estimates SAR model from log-abundance matrix of prab-object.
pop.sim
p-value simulation for presence-absence matrices clustering test
geo2neighbor
Neighborhood list from geographical distance
prabclus-package
prabclus package overview
lociplots
Visualises clusters of markers vs. species
prabclust
Clustering for biotic elements or for species delimitation (mixture method)
prabinit
Presence-absence/abundance matrix initialization
nastats
Missing values statistics for matrix
alleleinit
Diploid loci matrix initialization
specgroups
Average within-group distances for given groups
alleledist
Shared allele distance for diploid loci
build.nblist
Generate spatial weights from prabclus neighborhood list
prabtest
Parametric bootstrap test for clustering in presence-absence matrices
jaccard
Jaccard distance matrix
cluspop.nb
Simulation of presence-absence matrices (clustered)
kulczynski
Kulczynski distance matrix
waterdist
Overwater distances between islands in the Aegean sea
stressvals
Stress values for different dimensions of Kruskal's MDS
toprab
Convert abundance matrix into presence/absence matrix
tetragonula
Microsatellite genetic data of Tetragonula bees
NNclean
Nearest neighbor based clutter/noise detection
abundtest
Parametric bootstrap test for clustering in abundance matrices
con.regmat
Connected regions per species
phipt
Distances between communities, auxiliary functions
nn
Mean distance to kth nearest neighbor
randpop.nb
Simulation of presence-absence matrices (non-clustered)
qkulczynski
Quantitative Kulczynski distance matrix
coord2dist
Geographical coordinates to distances
regpop.sar
Simulation of abundance matrices (non-clustered)
siskiyou
Herbs of the Siskiyou Mountains
distratio
Distance ratio test statistics for distance based clustering
geco
geco distance matrix
nbtest
Test of neighborhood list
regdistbetweenone
Testing equality of one within-group and between-two groups distances regression
nb
Neighborhood list for Aegean islands
veronica
Genetic AFLP data of Veronica plants
unbuild.charmatrix
Internal: create allele list out of character matrix
regdistdiff
Regression difference between within-group dissimilarities
build.charmatrix
Internal: create character matrix out of allele list
build.ext.nblist
Internal: generates neighborhood list for diploid loci
alleleconvert
Format conversion for codominant marker data
comp.test
Compare species clustering and species groups
con.comp
Connectivity components of an undirected graph
dicedist
Dice distance matrix
crmatrix
Region-wise cluster membership