{ "_id": "6abb237099f7aa8c6aa43576", "Package": "codyn", "Title": "Community Dynamics Metrics", "Version": "2.0.6", "Authors@R": "c(person(\"Lauren\", \"Hallett\", email=\"lauren.m.hallett@gmail.com\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-0718-0257\")),\nperson(\"Meghan L.\", \"Avolio\", email=\"meghan.avolio@jhu.edu\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-2649-9159\")),\nperson(\"Ian T.\", \"Carroll\", email=\"carroll.ian@gmail.com\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-3616-810X\")),\nperson(\"Sydney K.\", \"Jones\", email=\"syd@sevilleta.unm.edu\", role=c(\"aut\")),\nperson(\"A. Andrew M.\", \"MacDonald\", email=\"a.a.m.macdonald@gmail.com\", role=c(\"aut\"), comment=c(ORCID = \"0000-0003-1162-169X\")),\nperson(\"Dan F. B.\", \"Flynn\", email=\"flynn@fas.harvard.edu\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-2978-5257\")),\nperson(\"Peter\", \"Slaughter\", email=\"slaughter@nceas.ucsb.edu\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-2192-403X\")),\nperson(\"Julie\", \"Ripplinger\", email=\"julie.ripplinger@asu.edu\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-2771-6637\")),\nperson(\"Scott L.\", \"Collins\", email=\"scollins@sevilleta.unm.edu\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-0193-2892\")),\nperson(\"Corinna\", \"Gries\", email=\"cgries@wisc.edu\", role=c(\"aut\"), comment=c(ORCID = \"0000-0002-9091-6543\")),\nperson(\"Matthew B.\", \"Jones\", email=\"jones@nceas.ucsb.edu\", role=c(\"aut\", \"cre\"), comment=c(ORCID = \"0000-0003-0077-4738\")))", "Date": "2026-09-17", "Description": "Univariate and multivariate temporal and spatial diversity\nindices, rank abundance curves, and community stability\nmeasures. The functions implement measures that are either\nexplicitly temporal and include the option to calculate them\nover multiple replicates, or spatial and include the option to\ncalculate them over multiple time points. Functions fall into\nfive categories: static diversity indices, temporal diversity\nindices, spatial diversity indices, rank abundance curves, and\ncommunity stability measures. The diversity indices are\ntemporal and spatial analogs to traditional diversity indices.\nSpecifically, the package includes functions to calculate\ncommunity richness, evenness and diversity at a given point in\nspace and time. In addition, it contains functions to calculate\nspecies turnover, mean rank shifts, and lags in community\nsimilarity between two time points. Details of the methods are\navailable in Hallett et al. (2016)\n and Avolio et al. (2019)\n.", "Encoding": "UTF-8", "License": "Apache License (== 2.0)", "URL": "https://github.com/NCEAS/codyn/, https://nceas.github.io/codyn/", "BugReports": "https://github.com/NCEAS/codyn/issues", "LazyData": "true", "VignetteBuilder": "knitr", "Config/Needs/website": "pkgdown", "Config/roxygen2/version": "8.1.0", "Repository": "https://nceas.r-universe.dev", "Date/Publication": "2026-09-29 00:33:14 UTC", "RemoteUrl": "https://github.com/NCEAS/codyn", "RemoteRef": "HEAD", "RemoteSha": "0a1d161e9adec8f650f5d695679bd5a812f2b4e1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-29 02:27:54 UTC", "User": "root" }, "Author": "Lauren Hallett [aut] (ORCID: ),\nMeghan L. Avolio [aut] (ORCID: ),\nIan T. Carroll [aut] (ORCID: ),\nSydney K. Jones [aut],\nA. Andrew M. MacDonald [aut] (ORCID:\n),\nDan F. B. Flynn [aut] (ORCID: ),\nPeter Slaughter [aut] (ORCID: ),\nJulie Ripplinger [aut] (ORCID: ),\nScott L. Collins [aut] (ORCID: ),\nCorinna Gries [aut] (ORCID: ),\nMatthew B. Jones [aut, cre] (ORCID:\n)", "Maintainer": "Matthew B. Jones ", "_user": "nceas", "_type": "src", "_file": "codyn_2.0.6.tar.gz", "_fileid": "https://r2.ropensci.org/e6ca3d602670d3d5152963258de796da8a455e7de73da4e7e9670017cd4533e4", "_filesize": 1092721, "_sha256": "e6ca3d602670d3d5152963258de796da8a455e7de73da4e7e9670017cd4533e4", "_expires": "2027-01-07T02:33:17.000Z", "_created": "2026-09-29T02:27:54.000Z", "_published": "2026-09-29T02:33:20.094Z", "_jobs": [ { "job": 109228291566, "time": 197, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11009741666" }, { "job": 109228291563, "time": 188, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11010336481" }, { "job": 109228291610, "time": 200, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "11009482017" }, { "job": 109228291613, "time": 180, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "11009567966" }, { "job": 109227187668, "time": 269, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "11009481597" }, { "job": 109228291500, "time": 139, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "11009586682" }, { "job": 109228291691, "time": 138, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "11009662713" }, { "job": 109228291579, "time": 138, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "11010137042" }, { "job": 109228291596, "time": 126, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "11010396062" } ], "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/nceas/actions/runs/36512373212", "_status": "success", "_upstream": "https://github.com/NCEAS/codyn", "_commit": { "id": "0a1d161e9adec8f650f5d695679bd5a812f2b4e1", "author": "Matt Jones ", "committer": "Matt Jones ", "message": "Commit citation updates directly to main with the NCEAS GitHub App (#136)\n\nReplace the monthly pull request with a direct commit to main, pushed\nwith a token from the NCEAS GitHub App so it can bypass branch protection\nand trigger the pkgdown site rebuild. The commit message lists the added\nand removed publications with their OpenAlex IDs, for use in\nexclude_works if one is a false match.\n\nCo-Authored-By: Claude Opus 5.5 \n", "time": 1790641994 }, "_maintainer": { "name": "Matthew B. Jones", "email": "jones@nceas.ucsb.edu", "login": "mbjones", "orcid": "0000-0003-0077-4738", "description": "", "uuid": 766407 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2.0", "role": "Depends" }, { "package": "assertthat", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "permute", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "testthat", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "pillar", "role": "Suggests" }, { "package": "reshape2", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "dplyr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" } ], "_owner": "nceas", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-38", "n": 10 }, { "week": "2026-40", "n": 10 } ], "_tags": [ { "name": "2.0.6", "date": "2026-09-18" } ], "_topics": [ "community-dynamics", "ecology", "spatial-dynamics", "temporal-dynamics" ], "_stars": 37, "_contributors": [ { "user": "laurenmh", "count": 218, "uuid": 6607034 }, { "user": "mbjones", "count": 209, "uuid": 766407 }, { "user": "aammd", "count": 201, "uuid": 1198242 }, { "user": "mavolio", "count": 82, "uuid": 15056076 }, { "user": "cgries", "count": 41, "uuid": 6526414 }, { "user": "gothub", "count": 35, "uuid": 6412946 }, { "user": "flynn-d", "count": 32, "uuid": 34866670 }, { "user": "sydjones", "count": 30, "uuid": 6425676 }, { "user": "itcarroll", "count": 20, "uuid": 3383837 }, { "user": "gavinsimpson", "count": 1, "uuid": 514696 }, { "user": "jameslamb", "count": 1, "uuid": 7608904 } ], "_userbio": { "uuid": 2159348, "type": "organization", "name": "National Center for Ecological Analysis and Synthesis", "followers": 92 }, "_downloads": { "count": 641, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/codyn" }, "_mentions": 11, "_devurl": "https://github.com/nceas/codyn", "_pkgdown": "https://nceas.github.io/codyn/", "_searchresults": 280, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/codyn.html", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md" ], "_homeurl": "https://github.com/nceas/codyn", "_realowner": "nceas", "_cranurl": true, "_releases": [ { "version": "1.0.0", "date": "2015-10-20" }, { "version": "1.0.1", "date": "2016-01-15" }, { "version": "1.1.0", "date": "2016-04-27" }, { "version": "2.0.0", "date": "2018-06-12" }, { "version": "2.0.1", "date": "2019-03-08" }, { "version": "2.0.2", "date": "2019-04-09" }, { "version": "2.0.3", "date": "2019-09-17" }, { "version": "2.0.4", "date": "2020-05-06" }, { "version": "2.0.5", "date": "2020-12-01" }, { "version": "2.0.6", "date": "2026-09-18" } ], "_exports": [ "abundance_change", 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"relative_cover" ], "rows": 1232, "table": true, "tojson": true } ], "_help": [ { "page": "abundance_change", "title": "Species Abundance Changes", "topics": [ "abundance_change" ] }, { "page": "abundance_difference", "title": "Abundance Differences", "topics": [ "abundance_difference" ] }, { "page": "collins08", "title": "Konza data from Collins et al. 2008", "topics": [ "collins08" ] }, { "page": "community_diversity", "title": "Community Diversity", "topics": [ "community_diversity" ] }, { "page": "community_stability", "title": "Community Stability", "topics": [ "community_stability" ] }, { "page": "community_structure", "title": "Community Structure", "topics": [ "community_structure" ] }, { "page": "confint.cyclic_shift", "title": "Confidence Intervals from a Cyclic Shift Permutation", "topics": [ "confint.cyclic_shift" ] }, { "page": "curve_change", "title": "Curve Change", "topics": [ "curve_change" ] }, { "page": "curve_difference", "title": "Curve Difference", "topics": [ "curve_difference" ] }, { "page": "cyclic_shift", "title": "Cyclic Shift Permutations", "topics": [ "cyclic_shift", "temporal_torus_translation" ] }, { "page": "knz_001d", "title": "Data from Konza Prairie, watershed 001d", "topics": [ "knz_001d" ] }, { "page": "mean_rank_shift", "title": "Mean Rank Shifts", "topics": [ "mean_rank_shift" ] }, { "page": "multivariate_change", "title": "Using dissimilarity-based measures to calculate changes in composition and dispersion", "topics": [ "multivariate_change" ] }, { "page": "multivariate_difference", "title": "Using dissimilarity-based measures to calculate differences in composition and dispersion between pairs of treatments at a single time point", "topics": [ "multivariate_difference" ] }, { "page": "pplots", "title": "Phosphorus plots data from Avolio et al. 2014", "topics": [ "pplots" ] }, { "page": "RAC_change", "title": "Rank Abundance Curve Changes", "topics": [ "RAC_change" ] }, { "page": "RAC_difference", "title": "Rank Abundance 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