Package: recluster 3.3

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

The analysis of different aspects of biodiversity requires specific algorithms. For example, in regionalisation analyses, the high frequency of ties and zero values in dissimilarity matrices produced by Beta-diversity turnover produces hierarchical cluster dendrograms whose topology and bootstrap supports are affected by the order of rows in the original matrix. Moreover, visualisation of biogeographical regionalisation can be facilitated by a combination of hierarchical clustering and multi-dimensional scaling. The recluster package provides robust techniques to visualise and analyse pattern of biodiversity and to improve occurrence data for cryptic taxa.

Authors:Leonardo Dapporto, Matteo Ramazzotti, Simone Fattorini, Roger Vila, Gerard Talavera, Roger H.L. Dennis

recluster_3.3.tar.gz
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recluster.pdf |recluster.html✨
recluster/json (API)

# Install 'recluster' in R:
install.packages('recluster', repos = c('https://leondap.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/leondap/recluster/issues

Datasets:
  • 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.
  • 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

On CRAN:

4.67 score 4 stars 39 scripts 545 downloads 3 mentions 30 exports 83 dependencies

Last updated 14 days agofrom:041ebb505b. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winERRORNov 09 2024
R-4.5-linuxERRORNov 09 2024
R-4.4-winERRORNov 09 2024
R-4.4-macERRORNov 09 2024
R-4.3-winERRORNov 09 2024
R-4.3-macERRORNov 09 2024

Exports:ah2sfbiodecryptbiodecrypt.crossbiodecrypt.optimisebiodecrypt.plotbiodecrypt.viewbiodecrypt.wraprecluster.bootrecluster.colrecluster.consrecluster.distrecluster.explrecluster.expl.dissrecluster.fstrecluster.fst.pairrecluster.group.colrecluster.histrecluster.identify.nodesrecluster.linerecluster.multirecluster.node.strengthrecluster.plotrecluster.plot.colrecluster.plot.matrixrecluster.plot.pierecluster.plot.sites.colrecluster.procrustesrecluster.regionrecluster.rotaterecluster.test.dist

Dependencies:alphahullapeclassclassIntcliclusterclusterGenerationcodacodetoolscolorspacecombinatcpp11DBIdeldirDEoptimdigestdoParallele1071expmfansifarverfastmatchforeachgenericsggplot2gluegtableigraphinterpisobanditeratorsKernSmoothlabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellnlmenumDerivoptimParallelpermutephangornphytoolspicantepillarpkgconfigplotrixpolyclipproxyquadprogR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppEigenrlangs2scalesscatterplot3dsfsgeostatspspatstat.dataspatstat.geomspatstat.randomspatstat.univarspatstat.utilssplancstibbleunitsutf8vctrsveganviridisLitewithrwk

Readme and manuals

Help Manual

Help pageTopics
An algorithm to attribute unidentified occurrence data based on a subset of identified recordsbiodecrypt
Perform a cross validation analysis to test the attribution of biodecrypt on attributed recordsbiodecrypt.cross
Comparing the values obtained by biodecrypt.wrap, it optimises the combination of alpha, buffer and ratio values to be used with biodecrypt function.biodecrypt.optimise
Plotting biodecrypt and biodecrypt.cross results.biodecrypt.plot
A function to view the hulls and manually adjust alpha values before applying biodecryptbiodecrypt.view
Wraps the biodecrypt.cross analysis to compare the performance of biodecrypt among different parameters.biodecrypt.wrap
West Mediterranean island butterflies provided with the package reclusterdataisl
Virtual island faunas provided with the package reclusterdatamod
A multiboot result obtained with the dataisl dataset.multiboot
Ordination methods for biodiversity patterns.reCluster recluster
Bootstrap nodes of consensus treesrecluster.boot
Projecting a two dimensional plot in RGB spacerecluster.col
Consensus tree among re-sampled treesrecluster.cons
Compute a dissimilarity matrix using a battery of beta-diversity indicesrecluster.dist
Computes the dissimilarity contained in a distance matrix which is explained by a clustering solution.recluster.expl
Cuts a phylogenetic tree and provides cluster membership of areas for custom of all possible clustering solutions and their explained dissimilarity.recluster.expl.diss
Compute some indexes of genetic differentiationrecluster.fst
Compute pairwise indexes of genetic differentiation among populationsrecluster.fst.pair
Computes mean coordinate values and RGB colours.recluster.group.col
Histogram of dissimilarity with tied and zero valuesrecluster.hist
Evaluating solutions in multiscale bootstraprecluster.identify.nodes
Identifies a line in a configuration and computes its intercept and angular coefficientrecluster.line
Multiscale bootstrap based on a consensus treerecluster.multi
Evaluating order row bias in a clusterrecluster.node.strength
A plotter for recluster bootstrapped objectsrecluster.plot
Plotting data in RGB spacerecluster.plot.col
Plot the values of the cells of a matrix in grey scalerecluster.plot.matrix
Plotting pies with RGB colours on a custom coordinate spacerecluster.plot.pie
Plotting RGB dots on a custom coordinate spacerecluster.plot.sites.col
Computes a procrustes analysis between two matrices even if only a subset of cases are shared.recluster.procrustes
A clustering method based on continuous consensus among clustering solutions after resampling row order.recluster.region
Rotates a bidimensional configuration according to a linerecluster.rotate
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.recluster.test.dist
Phylogenetic tree for the butterfly species included in dataisl datasettreebut
Hypothetical phylogenetic tree for the virtual island faunas provided with the package reclustertreemod