Package: betapart 1.6

Andres Baselga

betapart: Partitioning Beta Diversity into Turnover and Nestedness Components

Functions to compute pair-wise dissimilarities (distance matrices) and multiple-site dissimilarities, separating the turnover and nestedness-resultant components of taxonomic (incidence and abundance based), functional and phylogenetic beta diversity.

Authors:Andres Baselga [aut, cre], David Orme [aut], Sebastien Villeger [aut], Julien De Bortoli [aut], Fabien Leprieur [aut], Maxime Logez [aut], Sara Martinez-Santalla [aut], Ramiro Martin-Devasa [aut], Carola Gomez-Rodriguez [aut], Rosa M. Crujeiras [aut], Renato Henriques-Silva [ctb]

betapart_1.6.tar.gz
betapart_1.6.tar.gz(r-4.5-noble)betapart_1.6.tar.gz(r-4.4-noble)
betapart_1.6.tgz(r-4.4-emscripten)betapart_1.6.tgz(r-4.3-emscripten)
betapart.pdf |betapart.html✨
betapart/json (API)
NEWS

# Install 'betapart' in R:
install.packages('betapart', repos = 'https://cloud.r-project.org')
Datasets:
  • bbs1980 - BBS data by state for two timeslices
  • bbs2000 - BBS data by state for two timeslices
  • betatest - A data set of 4 communities, 107 species and a 4D functional space
  • ceram.n - Cerambycidae from Northern European Countries
  • ceram.s - Cerambycidae from Southern European Countries
  • coords.n - Spatial coordinates for Southern European Countries
  • coords.s - Spatial coordinates for Southern European Countries

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.97 score 2 stars 6 packages 2.6k downloads 111 mentions 27 exports 27 dependencies

Last updated 2 years agofrom:5a785771c8. Checks:1 OK, 2 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 15 2025
R-4.5-linuxNOTEMar 15 2025
R-4.4-linuxNOTEMar 15 2025

Exports:beta.multibeta.multi.abundbeta.pairbeta.pair.abundbeta.para.controlbeta.samplebeta.sample.abundbeta.tempbetapart.corebetapart.core.abundboot.coefs.decaybray.partdecay.modelfunctional.beta.multifunctional.beta.pairfunctional.betapart.corefunctional.betapart.core.pairwiseinter_geominter_geom_coordinter_rcddinter_rcdd_coordphylo.beta.multiphylo.beta.pairphylo.betapart.coreplot.decayqhull.optzdep

Dependencies:abindapeclustercodetoolsdigestdoSNOWfastmatchforeachgeometryiteratorsitertoolslatticelinproglpSolvemagicMASSMatrixmgcvminpack.lmnlmepermutepicantercddRcppRcppProgresssnowvegan

Citation

To cite package ‘betapart’ in publications use:

Baselga A, Orme D, Villeger S, De Bortoli J, Leprieur F, Logez M, Martinez-Santalla S, Martin-Devasa R, Gomez-Rodriguez C, Crujeiras R (2023). betapart: Partitioning Beta Diversity into Turnover and Nestedness Components. R package version 1.6, https://CRAN.R-project.org/package=betapart.

Corresponding BibTeX entry: 

  @Manual{,
    title = {betapart: Partitioning Beta Diversity into Turnover and
      Nestedness Components},
    author = {Andres Baselga and David Orme and Sebastien Villeger and
      Julien {De Bortoli} and Fabien Leprieur and Maxime Logez and Sara
      Martinez-Santalla and Ramiro Martin-Devasa and Carola
      Gomez-Rodriguez and Rosa M. Crujeiras},
    year = {2023},
    note = {R package version 1.6},
    url = {https://CRAN.R-project.org/package=betapart},
  }

Readme and manuals

Help Manual

Help pageTopics
BBS data by state for two timeslicesbbs1980 bbs2000 bbsData
Multiple-site dissimilaritiesbeta.multi
Abundance-based multiple-site dissimilaritiesbeta.multi.abund
Incidence-based pair-wise dissimilaritiesbeta.pair
Abundance-based pair-wise dissimilaritiesbeta.pair.abund
Specifying Control Values for Internal Parallel Clusterbeta.para.control
Resampling multiple-site dissimilarity for n sitesbeta.sample
Resampling abundance-based multiple-site dissimilarity for n sitesbeta.sample.abund
Temporal change in community compositionbeta.temp
Partitioning beta diversity into turnover and nestedness componentsbetapart-package betapart
Core calculations of betapartbetapart.core
Core calculations of betapart for abundance-based dissimilarity measuresbetapart.core.abund
A data set of 4 communities, 107 species and a 4D functional spacebetatest
Bootstrapping the parameters of distance-decay models computed with decay.model()boot.coefs.decay
Partitioning pair-wise Bray-Curtis dissimilaritiesbray.part
Cerambycidae from Northern European Countriesceram.n
Cerambycidae from Southern European Countriesceram.s
Spatial coordinates for Southern European Countriescoords.n
Spatial coordinates for Southern European Countriescoords.s
Fitting distance decay models to pair-wise assemblage similaritydecay.model
Multiple-site functional dissimilaritiesfunctional.beta.multi
Pair-wise functional dissimilaritiesfunctional.beta.pair
Core calculations of functional dissimilarities metricsfunctional.betapart.core
functional.betapart.core.pairwisefunctional.betapart.core.pairwise
Internal function to compute convexhull volumeinter_geom
Internal function to compute convexhull volume and vertice coordinatesinter_geom_coord
Internal function to compute convexhull volumeinter_rcdd
Internal function to compute convexhull volume and vertice coordinatesinter_rcdd_coord
Multiple-site phylogenetic dissimilaritiesphylo.beta.multi
Pair-wise phylogenetic dissimilaritiesphylo.beta.pair
Core calculations of phylogenetic dissimilarities metricsphylo.betapart.core
Plotting distance decay curves from models computed with decay.model()plot.decay
Specifying control Values for convexhull volume estimationqhull.opt
Assessing the differences between parameters of two distance-decay models computed with decay.model().zdep