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

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

## Documentation for package ‘prabclus’ version 2.3-4

- DESCRIPTION file.

## Help Pages

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