Ordination Methods for the Analysis of Beta-Diversity Indices

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Documentation for package ‘recluster’ version 3.5

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biodecrypt An algorithm to attribute unidentified occurrence data based on a subset of identified records
biodecrypt.cross Perform a cross validation analysis to test the attribution of biodecrypt on attributed records
biodecrypt.optimise Comparing the values obtained by biodecrypt.wrap, it optimises the combination of alpha, buffer and ratio values to be used with biodecrypt function.
biodecrypt.plot Plotting biodecrypt and biodecrypt.cross results.
biodecrypt.view A function to view the hulls and manually adjust alpha values before applying biodecrypt
biodecrypt.wrap Wraps the biodecrypt.cross analysis to compare the performance of biodecrypt among different parameters.
dataisl West Mediterranean island butterflies provided with the package recluster
datamod Virtual island faunas provided with the package recluster
multiboot A multiboot result obtained with the dataisl dataset.
reCluster Ordination methods for biodiversity patterns.
recluster Ordination methods for biodiversity patterns.
recluster.boot Bootstrap nodes of consensus trees
recluster.col Projecting a two dimensional plot in RGB space
recluster.cons Consensus tree from row-order permutations of a dissimilarity matrix
recluster.dist Compute a dissimilarity matrix using a battery of beta-diversity indices
recluster.expl Computes the dissimilarity contained in a distance matrix which is explained by a clustering solution.
recluster.expl.diss Cuts a phylogenetic tree and provides cluster membership of areas for custom of all possible clustering solutions and their explained dissimilarity.
recluster.fst Compute some indexes of genetic differentiation
recluster.fst.pair Compute pairwise indexes of genetic differentiation among populations
recluster.group.col Computes mean coordinate values and RGB colours.
recluster.hist Histogram of dissimilarity with tied and zero values
recluster.identify.nodes Evaluating solutions in multiscale bootstrap
recluster.line Identifies a line in a configuration and computes its intercept and angular coefficient
recluster.multi Multiscale bootstrap based on a consensus tree
recluster.node.strength Evaluating order row bias in a cluster
recluster.plot A plotter for recluster bootstrapped objects
recluster.plot.col Plotting data in RGB space
recluster.plot.matrix Plot the values of the cells of a matrix in grey scale
recluster.plot.pie Plotting pies with RGB colours on a custom coordinate space
recluster.plot.sites.col Plotting RGB dots on a custom coordinate space
recluster.procrustes Computes a procrustes analysis between two matrices even if only a subset of cases are shared.
recluster.region Consensus-based regionalisation from repeated row-order resampling
recluster.rotate Rotates a bidimensional configuration according to a line
recluster.test.dist Test variation lost by a bidimensional configuration when the coordinates of the elements are reduced to the configuration of the barycentres of a given series of groups.
treebut Phylogenetic tree for the butterfly species included in dataisl dataset
treemod Hypothetical phylogenetic tree for the virtual island faunas provided with the package recluster