R: Ordination Methods for the Analysis of Beta-Diversity Indices

# Ordination Methods for the Analysis of Beta-Diversity Indices

## Documentation for package ‘recluster’ version 3.5

- DESCRIPTION file
- Package README

## Help Pages

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