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

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Beta-diversity indices provide dissimilarity matrices with particular distribution of data requiring specific treatment. For example the high frequency of ties and zero values in turnover indices produces hierarchical cluster dendrograms whose topology and bootstrap supports are affected by the order of rows in the original matrix. Moreover, biogeographical regionalization can be facilitated by a combination of hierarchical clustering and multi-dimensional scaling. The recluster package provides robust techniques to analyze pattern of similarity in species composition.

Author
Leonardo Dapporto, Matteo Ramazzotti, Simone Fattorini, Roger Vila, Gerard Talavera, Roger H.L. Dennis
Date of publication
2015-03-06 21:11:09
Maintainer
Leonardo Dapporto <leondap@gmail.com>
License
GPL (>= 2.0)
Version
2.8
URLs

View on CRAN

Man pages

dataisl
West Mediterranean island butterflies provided with the...
datamod
Virtual island faunas provided with the package recluster
multiboot
A multiboot result from dataisl dataset.
recluster
Ordination methods for the analysis of beta-diversity...
recluster.boot
Bootstrap nodes of consensus trees
recluster.check
An internal workaround for the new ape package
recluster.col
Projecting a two dimensional plot in RGB space
recluster.cons
Consensus tree among re-sampled trees
recluster.dist
Compute a dissimilarity matrix using a battery of...
recluster.expl
Compute the dissimilarity contained in a distance matrix...
recluster.expl.diss
Cut a phylogenetic tree to a given series of nodes and...
recluster.group.col
Compute mean coordinate values and RGB colours.
recluster.hist
Histogram with tied and zero values
recluster.identify.nodes
Evaluating solutions in multiscale bootstrap
recluster.line
Identifies a line in a configuration and computes its...
recluster.multi
Multiscale bootstrap based on consensus trees
recluster.node.strength
Evaluating order row bias in a cluster
recluster.phybetadiv
An series of function for phylogenetic beta diversity
recluster.plot
A plotter for recluster bootstrapped objects
recluster.plot.col
Plotting data in RGB space
recluster.plot.matrix
Plot cell values of a matrix in grey scale
recluster.plot.sites.col
Plotting RGB dots on a custom coordinate space
recluster.procrustes
Compute a procrustes analysis between two matrices even if...
recluster.region
A new clustering method based on continuous consensus.
recluster.rotate
Rotates a bidimensional configuration according to a line
recluster.test.dist
Test variation lost by a bidimensional configuration when the...
treebut
Phylogenetic tree for the butterfly species included in...
treemod
Hypothetical phylogenetic tree for the virtual island faunas...

Files in this package

recluster
recluster/NAMESPACE
recluster/data
recluster/data/dataisl.rda
recluster/data/multiboot.rda
recluster/data/treebut.rda
recluster/data/treemod.rda
recluster/data/datamod.rda
recluster/R
recluster/R/recluster.plot.sites.col.R
recluster/R/recluster.dist.R
recluster/R/recluster.identify.nodes.R
recluster/R/recluster.cons.R
recluster/R/recluster.hist.R
recluster/R/recluster.multi.R
recluster/R/dist.mat.R
recluster/R/recluster.plot.col.R
recluster/R/recluster.expl.R
recluster/R/pd2.R
recluster/R/recluster.group.col.R
recluster/R/beta.pd.utils.R
recluster/R/recluster.col.R
recluster/R/recluster.boot.R
recluster/R/recluster.check.R
recluster/R/betajac.pd.R
recluster/R/recluster.procrustes.R
recluster/R/recluster.plot.matrix.R
recluster/R/recluster.test.dist.R
recluster/R/recluster.rotate.R
recluster/R/unifrac.R
recluster/R/phylosor.R
recluster/R/recluster.region.R
recluster/R/betasor.pd.R
recluster/R/unifract.R
recluster/R/recluster.node.strength.R
recluster/R/phylosorpd.R
recluster/R/phylosort.R
recluster/R/unifracpd.R
recluster/R/recluster.expl.diss.R
recluster/R/recluster.plot.R
recluster/R/recluster.line.R
recluster/MD5
recluster/DESCRIPTION
recluster/man
recluster/man/dataisl.Rd
recluster/man/recluster.phybetadiv.Rd
recluster/man/recluster.plot.sites.col.Rd
recluster/man/recluster.rotate.Rd
recluster/man/recluster.line.Rd
recluster/man/recluster.col.Rd
recluster/man/recluster.hist.Rd
recluster/man/recluster.dist.Rd
recluster/man/recluster.expl.Rd
recluster/man/recluster.plot.Rd
recluster/man/datamod.Rd
recluster/man/recluster.plot.col.Rd
recluster/man/recluster.identify.nodes.Rd
recluster/man/recluster.expl.diss.Rd
recluster/man/recluster.boot.Rd
recluster/man/recluster.node.strength.Rd
recluster/man/recluster.multi.Rd
recluster/man/treemod.Rd
recluster/man/recluster.cons.Rd
recluster/man/recluster.region.Rd
recluster/man/multiboot.Rd
recluster/man/recluster.plot.matrix.Rd
recluster/man/treebut.Rd
recluster/man/recluster.Rd
recluster/man/recluster.check.Rd
recluster/man/recluster.group.col.Rd
recluster/man/recluster.test.dist.Rd
recluster/man/recluster.procrustes.Rd