Functions for clustering of presence-absence and abundance data

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Documentation for package ‘prabclus’ version 2.1-4

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abundtest Parametric bootstrap test for clustering in abundance matrices
autoconst Spatial autocorrelation parameter estimation
autoreg Spatial autocorrelation parameter estimation
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
con.comp Connectivity components of an undirected graph
con.regmat Connected regions per species
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
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 test
prab Presence-absence/abundance matrix initialization
prab.sarestimate Estimates SAR model from log-abundance matrix of prab-object.
prabclust Clustering of species ranges from presence-absence matrices (mixture method)
prabinit Presence-absence/abundance matrix initialization
prabtest Parametric bootstrap test for clustering in presence-absence matrices
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 of species ranges from presence-absence matrices (mixture method)
print.summary.prabtest Print and summary method for prabtest
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
siskiyou.groups Herbs of the Siskiyou Mountains
siskiyou.nb Herbs of the Siskiyou Mountains
specgroups Average within-group distances for given groups
summary.prabtest Print and summary method for prabtest
toprab Convert abundance matrix into binary matrix
waterdist Overwater distances between islands in the Aegean sea