{ "_id": "6a1f391db401979e73428e95", "Package": "CNVRG", "Title": "Dirichlet-Multinomial Modelling of Relative Abundance Data", "Version": "1.0.1", "Authors@R": "c(person(given = \"Joshua\",\nfamily = \"Harrison\",\nrole = c(\"aut\", \"cre\"),\nemail = \"joshua.grant.harrison@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2524-0273\")),\nperson(given = \"Vivaswat\",\nfamily = \"Shastry\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-7294-5607\")),\nperson(given = \"W. John\",\nfamily = \"Calder\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-8923-1803\")),\nperson(given = \"C. Alex\",\nfamily = \"Buerkle\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0003-4222-8858\")))", "Maintainer": "Joshua Harrison ", "Description": "Implements Dirichlet multinomial modelling of relative\nabundance data using functionality provided by the 'Stan'\nsoftware. The purpose of this package is to provide a user\nfriendly way to interface with 'Stan' that is suitable for\nthose new to modelling. For more regarding the modelling\nmathematics and computational techniques we use see our\npublication in Molecular Ecology Resources titled \"Dirichlet\nmultinomial modelling outperforms alternatives for analysis of\necological count data\" (Harrison et al. 2020\n).", "License": "GPL-3", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.1.1", "Biarch": "true", "SystemRequirements": "GNU make", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-10 08:47:37 UTC", "User": "root" }, "Config/pak/sysreqs": "make", "Repository": "https://jharrisonecoevo.r-universe.dev", "Date/Publication": "2025-03-25 03:38:00 UTC", "RemoteUrl": "https://github.com/jharrisonecoevo/cnvrg", "RemoteRef": "HEAD", "RemoteSha": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "Author": "Joshua Harrison [aut, cre] (ORCID:\n),\nVivaswat Shastry [aut] (ORCID: ),\nW. John Calder [aut] (ORCID: ),\nC. Alex Buerkle [aut] (ORCID: )", "MD5sum": "1598120a332649bf426001d4d7650aff", "_user": "jharrisonecoevo", "_type": "src", "_file": "CNVRG_1.0.1.tar.gz", "_fileid": "7fee360452fff0b6d569eb2ef27e1bcad26a237e4da018e8842ea42894a2a456", "_filesize": 153048, "_sha256": "7fee360452fff0b6d569eb2ef27e1bcad26a237e4da018e8842ea42894a2a456", "_created": "2026-05-10T08:47:37.000Z", "_published": "2026-06-02T20:12:13.582Z", "_distro": "noble", "_jobs": [ { "job": 79162482406, "time": 274, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "6902457208" }, { "job": 79162482024, "time": 269, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "6902456781" }, { "job": 79162482595, "time": 266, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "6902456467" }, { "job": 79162482578, "time": 274, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "6902457291" }, { "job": 79162482510, "time": 220, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "6902576706" }, { "job": 79162482605, "time": 560, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "6902567178" }, { "job": 79162482657, "time": 284, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "6902571828" }, { "job": 79162482108, "time": 507, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "6902613701" }, { "job": 79162481952, "time": 239, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6902428152" }, { "job": 79162481777, "time": 150, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79162482483, "time": 315, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "6902461377" }, { "job": 79162482807, "time": 302, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "6902460148" }, { "job": 79162482307, "time": 302, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "6902460083" } ], "_buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/jharrisonecoevo/cnvrg", "_commit": { "id": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "author": "Joshua Harrison ", "committer": "Joshua Harrison ", "message": "version bump\n", "time": 1742873880 }, "_maintainer": { "name": "Joshua Harrison", "email": "joshua.grant.harrison@gmail.com", "login": "jharrisonecoevo", "uuid": 29388325, "orcid": "0000-0003-2524-0273" }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.4.0", "role": "Depends" }, { "package": "BH", "version": ">= 1.66.0", "role": "LinkingTo" }, { "package": "Rcpp", "version": ">= 0.12.0", "role": "LinkingTo" }, { "package": "RcppEigen", "version": ">= 0.3.3.3.0", "role": "LinkingTo" }, { "package": "RcppParallel", "version": ">= 5.0.1", "role": "LinkingTo" }, { "package": "rstan", "version": ">= 2.26.0", "role": "LinkingTo" }, { "package": "StanHeaders", "version": ">= 2.26.0", "role": "LinkingTo" }, { "package": "methods", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.0", "role": "Imports" }, { "package": "rstan", "version": ">= 2.26.0", "role": "Imports" }, { "package": "vegan", "role": "Imports" }, { "package": "rstantools", "version": ">= 2.1.1", "role": "Imports" }, { "package": "tibble", "role": "Imports" } ], "_owner": "jharrisonecoevo", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 2, "_contributors": [ { "user": "jharrisonecoevo", "count": 2, "uuid": 29388325 }, { "user": "andrjohns", "count": 1, "uuid": 27717896 } ], "_userbio": { "uuid": 29388325, "type": "user", "name": "Josh Harrison" }, "_downloads": { "count": 224, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/CNVRG" }, "_devurl": "https://github.com/jharrisonecoevo/cnvrg", "_searchresults": 14, "_topics": [ "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/CNVRG.html", "extra/contents.json", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/jharrisonecoevo/cnvrg", "_realowner": "jharrisonecoevo", "_cranurl": true, "_releases": [ { "version": "0.1", "date": "2020-09-16" }, { "version": "0.2", "date": "2020-11-21" }, { "version": "1.0.0", "date": "2021-09-04" } ], "_exports": [ "cnvrg_HMC", "cnvrg_VI", "diff_abund", "diversity_calc", "extract_pi_quantiles", "extract_point_estimate", "indexer", "isd_transform" ], "_datasets": [ { "name": "fungi", "title": "Fungal endophytes of Astragalus lentiginosus grown near Reno, NV", "object": "fungi", "class": [ "data.frame" ], "fields": [ "treatment", "Otu4", "Otu58", "Otu77", "Otu86", "Otu9", "Otu11", "Otu10", "Otu54", "Otu42", "Otu40", "Otu74", "Otu12", "Otu72", "Otu79", "Otu96", "Otu94", "Otu6", "Otu92", "Otu70", "Otu71", "Otu97", "Otu62", "Otu7", "Otu99", "Otu76", "Otu100" ], "rows": 148, "table": true, "tojson": true } ], "_help": [ { "page": "CNVRG-package", "title": "The 'CNVRG' package.", "topics": [ "CNVRG-package", "CNVRG" ] }, { "page": "cnvrg_HMC", "title": "Perform Hamiltonian Monte Carlo sampling", "topics": [ "cnvrg_HMC" ] }, { "page": "cnvrg_VI", "title": "Perform variational inference sampling", "topics": [ "cnvrg_VI" ] }, { "page": "diff_abund", "title": "Calculate features with different abundances between treatment groups", "topics": [ "diff_abund" ] }, { "page": "diversity_calc", "title": "Calculate diversity entropies for each replicate", "topics": [ "diversity_calc" ] }, { "page": "extract_pi_quantiles", "title": "Extract quantiles of pi parameters", "topics": [ "extract_pi_quantiles" ] }, { "page": "extract_point_estimate", "title": "Extract point estimates of multinomial and Dirichlet parameters", "topics": [ "extract_point_estimate" ] }, { "page": "fungi", "title": "Fungal endophytes of Astragalus lentiginosus grown near Reno, NV", "topics": [ "fungi" ] }, { "page": "indexer", "title": "Determine indices for treatment groups", "topics": [ "indexer" ] }, { "page": "isd_transform", "title": "Transform data into estimates of absolute abundances using an ISD", "topics": [ "isd_transform" ] } ], "_readme": "https://github.com/jharrisonecoevo/cnvrg/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "callr", "checkmate", "cli", "cluster", "cpp11", "desc", "distributional", "farver", "generics", "ggplot2", "glue", "gridExtra", "gtable", "inline", "isoband", "labeling", "lattice", "lifecycle", "loo", "magrittr", "MASS", "Matrix", "matrixStats", "mgcv", "nlme", "numDeriv", "permute", "pillar", "pkgbuild", "pkgconfig", "posterior", "processx", "ps", "QuickJSR", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "rlang", "rstan", "rstantools", "S7", "scales", "StanHeaders", "tensorA", "tibble", "utf8", "vctrs", "vegan", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_score": 3.146128035678238, "_indexed": true, "_nocasepkg": "cnvrg", "_universes": [ "jharrisonecoevo" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-05-10T08:50:50.000Z", "distro": "noble", "arch": "aarch64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "08924ea07b5d8c2fae0606df76d40ae33a9f9f6e336a37b5d1d2ea007e9f9c2e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" }, { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-05-10T08:50:47.000Z", "distro": "noble", "arch": "x86_64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "d2b983f162a5b06fe59793d049cb228e6bc354b62e975358db212139d9a14ad0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" }, { "r": "4.6.0", "os": "linux", "version": "1.0.1", "date": "2026-05-10T08:50:46.000Z", "distro": "noble", "arch": "aarch64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "984c1b071ed0d790c12995fba8d8759fd48fbcce49e6c2f7d6eed96ced0b01d6", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" }, { "r": "4.6.0", "os": "linux", "version": "1.0.1", "date": "2026-05-10T08:50:49.000Z", "distro": "noble", "arch": "x86_64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "010dc98fd0ba6741fc0ca55a5cf438379503f688c8d8e2b5abc6b78d3421db1b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-05-10T09:12:35.000Z", "arch": "aarch64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "d821d840955dae393405266c9f2cfe1a3764695237aec3cd56eba3bfec29eb55", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-05-10T09:08:18.000Z", "arch": "x86_64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "99d77b30a14a8e499919944baa894c58c0cfb1d59dc6f67db781beaee2a191e5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" }, { "r": "4.6.0", "os": "mac", "version": "1.0.1", "date": "2026-05-10T09:10:57.000Z", "arch": "aarch64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "07cb1015a7bcf54e8c2acc24338fd2d8bda3fc835d9cebb415cf5194fbe4cee5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" }, { "r": "4.6.0", "os": "mac", "version": "1.0.1", "date": "2026-05-10T09:16:53.000Z", "arch": "x86_64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "93990f9994e6d35d959a15db60178490c606f9116edb1383173c89a4fbf58950", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-05-10T08:50:25.000Z", "arch": "x86_64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "ee703b2038266cac55c30432e199e20245ec1fc4a263bd3d91cb26a34fe71941", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" }, { "r": "4.5.3", "os": "win", "version": "1.0.1", "date": "2026-05-10T08:50:04.000Z", "arch": "x86_64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "405b5229b8f1571ec46969bf93f4626638e931ff6048e30da2c211819e3e58ee", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" }, { "r": "4.6.0", "os": "win", "version": "1.0.1", "date": "2026-05-10T08:50:11.000Z", "arch": "x86_64", "commit": "01cf0d0d69f9f56772df4bd981ab4fde2079bbb1", "fileid": "b7692fa5e75a9e55606537eec1163ded4c076b7ef6e76a365bbb70aae8877bae", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/jharrisonecoevo/actions/runs/25624353180" } ] }