prabclus (version 2.1-2)

prabclus-package: Test for clustering of presence-absence data ~~ package title ~~

Description

Distance-based parametric bootstrap tests for clustering, mainly intended for presence-absence data (clustering of species distribution maps). Jaccard, Kulczynski and geco distance measures, clustering of presence-absence and abundance data, and nearest neighbor based noise detection (R port of Byers and Raftery's (1998) "NNclean"). Main functions are prabtest (for testing), prabclust (for clustering), prabinit (for preparing the data) and NNclean (for noise detection). The help-pages for prabtest and prabclust contain simple standard executions. ~~ A concise (1-5 lines) description of the package ~~

Details

ll{ Package: prabclus Version: 2.0-2 Date: 2006-10-06 Depends: R (>= 2.0), MASS Suggests: mclust02 License: GPL URL: http://www.homepages.ucl.ac.uk/~ucakche Packaged: Fri Oct 6 20:57:45 2006; chrish Built: R 2.6.0; ; 2007-11-05 12:53:48; unix }

Index: NNclean Nearest neighbor based clutter/noise detection autoconst Spatial autocorrelation parameter estimation 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 piecewiselin Piecewise linear transformation for distance matrices pop.sim p-value simulation for presence-absence matrices clustering test 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 qkulczynski Quantitative Kulczynski distance matrix randpop.nb Simulation of presence-absence matrices (non-clustered) summary.prabtest Print and summary method for prabtest waterdist Overwater distances between islands in the Aegean sea ~~ An overview of how to use the package, including the most important ~~ ~~ functions ~~

References

~~ Literature or other references for background information ~~

See Also

~~ Optional links to other man pages, e.g. ~~ ~~ ~~

Examples

~~ simple examples of the most important functions ~~