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

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Documentation for package ‘prabclus’ version 2.3-4

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prabclus-package prabclus package overview
abundtest Parametric bootstrap test for clustering in abundance matrices
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
alleleobject Diploid loci matrix initialization
allelepaircomp Internal: compares two pairs of alleles
autoconst Spatial autocorrelation parameter estimation
autoreg 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
cfchord Distances between communities, auxiliary functions
cluspop.nb Simulation of presence-absence matrices (clustered)
communities Construct communities from individuals
communitydist Distances between communities
comp.test Compare species clustering and species groups
con.comp Connectivity components of an undirected graph
con.regmat Connected regions per species
coord2dist Geographical coordinates to distances
crmatrix Region-wise cluster membership
dicedist Dice distance matrix
diploidcomlist Distances between communities, auxiliary functions
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 clustering
hprabclust Clustering of species ranges from presence-absence matrices (hierarchical methods)
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
phipt Distances between communities, auxiliary functions
piecewiselin Piecewise linear transformation for distance matrices
plotdistreg Plots for within-groups and between-groups distance regression
pop.sim p-value simulation for presence-absence matrices clustering test
prab Presence-absence/abundance matrix initialization
prab.sarestimate Estimates SAR model from log-abundance matrix of prab-object.
prabclust Clustering for biotic elements or for species delimitation (mixture method)
prabinit Presence-absence/abundance matrix initialization
prabtest Parametric bootstrap test for clustering in presence-absence matrices
print.alleleobject Diploid loci matrix initialization
print.comprabclust Clustering of species ranges from presence-absence matrices (hierarchical methods)
print.nnclean Nearest neighbor based clutter/noise detection
print.prab Presence-absence/abundance matrix initialization
print.prabclust Clustering for biotic elements or for species delimitation (mixture method)
print.regdistbetween Testing equality of within-groups and between-groups distances regression
print.regeqdist Testing equality of two distance-regressions
print.summary.prabtest Parametric bootstrap test for clustering in presence-absence matrices
qkulczynski Quantitative Kulczynski distance matrix
randpop.nb Simulation of presence-absence matrices (non-clustered)
regdist Regression between subsets of dissimilarity matrices
regdistbetween Testing equality of within-groups and between-groups distances regression
regdistbetweenone Testing equality of one within-group and between-two groups distances regression
regdistdiff Regression difference between within-group dissimilarities
regdistdiffone Regression difference within reference group and between-group dissimilarities
regeqdist Testing equality of two distance-regressions
regpop.sar Simulation of abundance matrices (non-clustered)
shared.problist Distances between communities, auxiliary functions
siskiyou Herbs of the Siskiyou Mountains
siskiyou.groups Herbs of the Siskiyou Mountains
siskiyou.nb Herbs of the Siskiyou Mountains
specgroups Average within-group distances for given groups
stressvals Stress values for different dimensions of Kruskal's MDS
summary.prabtest Parametric bootstrap test for clustering in presence-absence matrices
tetragonula Microsatellite genetic data of Tetragonula bees
tetragonula.coord 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
veronica.coord Genetic AFLP data of Veronica plants
waterdist Overwater distances between islands in the Aegean sea