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

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.

AuthorLeonardo Dapporto, Matteo Ramazzotti, Simone Fattorini, Roger Vila, Gerard Talavera, Roger H.L. Dennis
Date of publication2015-03-06 21:11:09
MaintainerLeonardo Dapporto <leondap@gmail.com>
LicenseGPL (>= 2.0)
Version2.8
http://www.unifi.it/scibio/bioinfo/recluster.html

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

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