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

abundtest | Parametric bootstrap test for clustering in abundance... |

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 |

allelepaircomp | Internal: compares two pairs of alleles |

autoconst | 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 |

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 |

concomp | Connectivity components of an undirected graph |

conregmat | Connected regions per species |

coord2dist | Geographical coordinates to distances |

crmatrix | Region-wise cluster membership |

dicedist | Dice distance matrix |

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... |

hprabclust | Clustering of species ranges from presence-absence matrices... |

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... |

pop.sim | p-value simulation for presence-absence matrices clustering... |

prabclus-package | prabclus package overview |

prabclust | Clustering for biotic elements or for species delimitation... |

prabinit | Presence-absence/abundance matrix initialization |

prab.sarestimate | Estimates SAR model from log-abundance matrix of prab-object. |

prabtest | Parametric bootstrap test for clustering in presence-absence... |

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... |

regdistbetweenone | Testing equality of one within-group and between-two groups... |

regdistdiff | Regression difference between within-group dissimilarities |

regdistdiffone | Regression difference within reference group and... |

regeqdist | Testing equality of two distance-regressions |

regpop.sar | Simulation of abundance matrices (non-clustered) |

siskiyou | Herbs of the Siskiyou Mountains |

specgroups | Average within-group distances for given groups |

stressvals | Stress values for different dimensions of Kruskal's MDS |

tetragonula | 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 |

waterdist | Overwater distances between islands in the Aegean sea |

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