{"Package":"rdiversity","Type":"Package","Title":"Measurement and Partitioning of Similarity-Sensitive\nBiodiversity","Version":"2.2.0","Date":"2022-04-29","Authors@R":"c(person(\"Sonia\", \"Mitchell\", email = \"sonia.mitchell@glasgow.ac.uk\",\nrole = c(\"aut\"), comment = c(ORCID = \"0000-0003-1536-2066\")),\nperson(\"Richard\", \"Reeve\", email = \"richard.reeve@glasgow.ac.uk\",\nrole = c(\"cre\", \"aut\", \"ths\"), comment = c(ORCID = \"0000-0003-2589-8091\")),\nperson(\"Tom\", \"White\", email = \"whitetomjames@gmail.com\",\nrole = \"ctb\", comment = c(ORCID = \"0000-0002-9639-3800\")),\nperson(\"Daniel\", \"Drrhfer\", email = \"ddo@openmailbox.org\", role = \"ctb\"),\nperson(\"Aaron\", \"Rudkin\", email = \"rudkin@ucla.edu\", role = \"ctb\"))","Maintainer":"Richard Reeve ","URL":"https://github.com/boydorr/rdiversity","BugReports":"https://github.com/boydorr/rdiversity/issues","Description":"Provides a framework for the measurement and partitioning of\nthe (similarity-sensitive) biodiversity of a metacommunity and its\nconstituent subcommunities. Richard Reeve, et al. (2016)\n.","License":"GPL-3","Depends":"R (>= 2.10)","Imports":"methods, reshape2, stats, stringdist, utils","Suggests":"ape, testthat, knitr, markdown, rmarkdown, covr","RoxygenNote":"7.1.2","Encoding":"UTF-8","VignetteBuilder":"knitr","Collate":"'ancestral_nodes.R' 'binary.R' 'chainsaw.R'\n'check_partition.R' 'check_phypartition.R' 'check_similarity.R'\n'class-distance.R' 'class-metacommunity.R' 'class-powermean.R'\n'class-relativeentropy.R' 'class-similarity.R'\n'descendant_tips.R' 'similarity.R' 'dist2sim.R' 'distance.R'\n'metadiv.R' 'subdiv.R' 'metacommunity.R'\n'diversity-components.R' 'diversity-measures.R' 'gen2dist.r'\n'geneid.R' 'genevec.R' 'hs_parameters.R' 'inddiv.R'\n'phy2branch.R' 'phy2dist.R' 'phy_abundance.R' 'phy_struct.R'\n'power_mean.R' 'powermean.R' 'rdiversity-package.R'\n'relativeentropy.R' 'repartition.R' 'smatrix.R' 'summarise.R'\n'tax2dist.R' 'taxfac.R' 'taxid.R' 'taxmask.R' 'taxvec.R'\n'tbar.R' 'zmatrix.R'","NeedsCompilation":"no","Packaged":"2022-05-05 23:28:39 UTC; richardr","Author":"Sonia Mitchell [aut] (),\nRichard Reeve [cre, aut, ths] (),\nTom White [ctb] (),\nDaniel Drrhfer [ctb],\nAaron Rudkin [ctb]","Repository":"CRAN","Date/Publication":"2022-05-06 07:00:02 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/rdiversity_2.2.0.tar.gz","jsonAuthors":[{"name":"Sonia Mitchell","email":"sonia.mitchell@glasgow.ac.uk","maintainer":false},{"name":"Richard Reeve","email":"richard.reeve@glasgow.ac.uk","maintainer":true},{"name":"Tom White","email":"whitetomjames@gmail.com","maintainer":false},{"name":"Daniel Drrhfer","email":"ddo@openmailbox.org","maintainer":false},{"name":"Aaron Rudkin","email":"rudkin@ucla.edu","maintainer":false}],"readme":"# rdiversity: diversity measurement in R \n[![](https://img.shields.io/badge/docs-rdiversity-blue)](https://boydorr.github.io/rdiversity/)\n[![test-build](https://github.com/boydorr/rdiversity/workflows/build/badge.svg)](https://github.com/boydorr/rdiversity/actions)\n[![codecov](https://codecov.io/gh/boydorr/rdiversity/branch/master/graph/badge.svg)](https://app.codecov.io/gh/boydorr/rdiversity)\n[![CodeFactor](https://www.codefactor.io/repository/github/boydorr/rdiversity/badge)](https://www.codefactor.io/repository/github/boydorr/rdiversity)\n[![License: GPL-3.0](https://img.shields.io/badge/licence-GPL--3-green)](https://opensource.org/licenses/GPL-3.0)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.597470.svg)](https://doi.org/10.5281/zenodo.597470)\n[![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/rdiversity?color=yellow)](https://cran.r-project.org/package=rdiversity)\n\n`rdiversity` is a package for R based around a framework for measuring biodiversity using similarity-sensitive diversity measures. It provides functionality for measuring alpha, beta and gamma diversity of metacommunities (*e.g.* ecosystems) and their constituent subcommunities, where similarity may be defined as taxonomic, phenotypic, genetic, phylogenetic, functional, and so on. It uses the diversity framework described in the arXiv paper [arXiv:1404.6520 (q-bio.QM)](https://arxiv.org/abs/1404.6520), \"How to partition diversity\". \n\nThis package has now reached a stable release and is cross-validated against our Julia package [Diversity.jl](https://github.com/EcoJulia/Diversity.jl), which is developed independently. Please [raise an issue](https://github.com/boydorr/rdiversity/issues) if you find any problems.\n\nTo install rdiversity from CRAN, simply run the following from an R console:\n\n```{r}\ninstall.packages(\"rdiversity\")\n```\n\nThe latest development version can be installed from GitHub:\n```{r]\n# install.packages(\"devtools\")\ndevtools::install_github(\"boydorr/rdiversity\")\n```\n\nExamples of how to use the package are included in our \n[docs](http://boydorr.github.io/rdiversity/articles/examples.html), as well \nas in a vignette currently only available in the development version of this package:\n\n```{r}\ninstall_github(\"boydorr/rdiversity\", build_vignettes = TRUE)\nvignette(\"examples\", \"rdiversity\")\n```","jobInfo":{"package":"rdiversity","version":"2.2.0","parsingStatus":"success","parserVersion":1,"parsedAt":"2022-05-06T09:30:28+0000"}}

Description

Usage

Arguments