{ "_id": "6a2e55053efcd9bda4309fcf", "Package": "occumb", "Title": "Site Occupancy Modeling for Environmental DNA Metabarcoding", "Version": "1.3.0", "Authors@R": "c(\nperson(\"Keiichi\", \"Fukaya\", , \"fukayak99@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Ken\", \"Kellner\", role = \"cph\",\ncomment = \"summary method for occumbFit class, processing of NIMBLE results, and print method for nimbleSummary class\"),\nperson(\"Mika\", \"Takahashi\", , \"takahashi.mika@nies.go.jp\", role = \"aut\"),\nperson(\"Martyn\", \"Plummer\", role = \"ctb\",\ncomment = \"fixes for JAGS 5.0.0 compatibility\"),\nperson(\"Koji\", \"Makiyama\", role = \"ctb\",\ncomment = \"option to use NIMBLE\"),\nperson(\"Kentaro\", \"Matsuura\", role = \"ctb\",\ncomment = \"option to use NIMBLE\")\n)", "Description": "Fits community site occupancy models to environmental DNA\nmetabarcoding data collected using spatially-replicated survey\ndesign. Model fitting results can be used to evaluate and\ncompare the effectiveness of species detection to find an\nefficient survey design. Reference: Fukaya et al. (2022)\n, Fukaya and Hasebe (2025)\n.", "License": "GPL (>= 3)", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.3.3", "Config/testthat/edition": "3", "Collate": "'classes.R' 'fish.R' 'fish_raw.R' 'get_posterior.R' 'gof.R'\n'nimbleSummary.R' 'occumbData.R' 'occumb.R' 'plot.R'\n'predict.R' 'run_nimble.R' 'show.R' 'summary.R' 'utility.R'\n'utils.R'", "URL": "https://fukayak.github.io/occumb/,\nhttps://github.com/fukayak/occumb", "VignetteBuilder": "knitr", "SystemRequirements": "JAGS (http://mcmc-jags.sourceforge.net)", "BugReports": "https://github.com/fukayak/occumb/issues", "Language": "en-US", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-14 07:11:59 UTC", "User": "root" }, "Author": "Keiichi Fukaya [aut, cre], Ken Kellner [cph] (summary method\nfor occumbFit class, processing of NIMBLE results, and print\nmethod for nimbleSummary class), Mika Takahashi [aut], Martyn\nPlummer [ctb] (fixes for JAGS 5.0.0 compatibility), Koji\nMakiyama [ctb] (option to use NIMBLE), Kentaro Matsuura [ctb]\n(option to use NIMBLE)", "Maintainer": "Keiichi Fukaya ", "Config/pak/sysreqs": "jags", "Repository": "https://cran.r-universe.dev", "Date/Publication": "2026-04-06 23:54:35 UTC", "RemoteUrl": "https://github.com/cran/occumb", "RemoteRef": "HEAD", "RemoteSha": "f19b843f6b713b18c7e5d53b3e0b112b0274b046", "MD5sum": "ec04b8e0efb03baed8698382702ab074", "_user": "cran", "_type": "src", "_file": "occumb_1.3.0.tar.gz", "_fileid": "37740ea2b6074097baeaeafd9f1fa030d4259c2c5850dcbf3d53dda101205633", "_filesize": 1141596, "_sha256": "37740ea2b6074097baeaeafd9f1fa030d4259c2c5850dcbf3d53dda101205633", "_created": "2026-06-14T07:11:59.000Z", "_published": "2026-06-14T07:15:17.721Z", "_distro": "noble", "_jobs": [ { "job": 81257655630, "time": 165, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7618546001" }, { "job": 81257655620, "time": 153, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7618544576" }, { "job": 81257462504, "time": 186, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7618525379" }, { "job": 81257655628, "time": 126, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7618540893" } ], "_buildurl": "https://github.com/r-universe/cran/actions/runs/27491442576", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/occumb", "_commit": { "id": "f19b843f6b713b18c7e5d53b3e0b112b0274b046", "author": "Keiichi Fukaya ", "committer": "cran-robot ", "message": "version 1.3.0\n", "time": 1775519675 }, "_maintainer": { "name": "Keiichi Fukaya", "email": "fukayak99@gmail.com", "login": "fukayak", "description": "", "uuid": 2058221 }, "_registered": true, "_dependencies": [ { "package": "jagsUI", "role": "Depends" }, { "package": "R", "version": ">= 2.10", "role": "Depends" }, { "package": "stats", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "checkmate", "role": "Imports" }, { "package": "crayon", "role": "Imports" }, { "package": "knitr", "role": "Imports" }, { "package": "covr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "tibble", "role": "Suggests" }, { "package": "vdiffr", "role": "Suggests" }, { "package": "nimble", "version": ">= 1.4.2", "role": "Suggests" }, { "package": "coda", "role": "Suggests" }, { "package": "parallel", "role": "Suggests" }, { "package": "DoE.base", "role": "Suggests" } ], "_owner": "cran", "_selfowned": false, "_usedby": 0, "_updates": [ { "week": "2025-29", "n": 1 }, { "week": "2026-02", "n": 1 }, { "week": "2026-15", "n": 1 } ], "_tags": [ { "name": "1.2.1", "date": "2025-07-16" }, { "name": "1.2.2", "date": "2026-01-09" }, { "name": "1.3.0", "date": "2026-04-06" } ], "_stars": 1, "_contributors": [ { "user": "fukayak", "count": 8, "uuid": 2058221 } ], "_userbio": { "uuid": 6899542, "type": "organization", "name": "cran", "followers": 606, "description": "Unofficial read-only mirror of all CRAN R packages" }, "_downloads": { "count": 529, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/occumb" }, "_devurl": "https://github.com/fukayak/occumb", "_pkgdown": "https://fukayak.github.io/occumb/", "_searchresults": 28, "_topics": [ "jags", "cpp" ], "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/NEWS.html", "extra/NEWS.txt", "extra/occumb.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/fukayak/occumb", "_realowner": "fukayak", "_cranurl": false, "_releases": [ { "version": "1.0.1", "date": "2023-09-23" }, { "version": "1.0.2", "date": "2023-10-19" }, { "version": "1.0.3", "date": "2024-01-08" }, { "version": "1.1.0", "date": "2024-03-26" }, { "version": "1.2.0", "date": "2025-05-27" }, { "version": "1.2.1", "date": "2025-07-16" }, { "version": "1.2.2", "date": "2026-01-09" }, { "version": "1.3.0", "date": "2026-04-06" } ], "_exports": [ "eval_util_L", "eval_util_R", "get_post_samples", "get_post_summary", "gof", "list_cond_L", "list_cond_R", "occumb", "occumbData", "plot", "predict", "summary" ], "_datasets": [ { "name": "fish", "title": "Fish eDNA metabarcoding dataset", "object": "fish", "class": [ "occumbData" ], "fields": [], "table": false, "tojson": false }, { "name": "fish_raw", "title": "Fish eDNA metabarcoding dataset", "object": "fish_raw", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "eval_util_L", "title": "Expected utility for local species diversity assessments.", "topics": [ "eval_util_L" ] }, { "page": "eval_util_R", "title": "Expected utility for regional species diversity assessments.", "topics": [ "eval_util_R" ] }, { "page": "fish", "title": "Fish eDNA metabarcoding dataset", "topics": [ "fish" ] }, { "page": "fish_raw", "title": "Fish eDNA metabarcoding dataset", "topics": [ "fish_raw" ] }, { "page": "get_posterior", "title": "Extract posterior samples or summary of parameters from a model-fit object.", "topics": [ "get_posterior", "get_post_samples", "get_post_summary" ] }, { "page": "gof", "title": "Goodness-of-fit assessment of the fitted model.", "topics": [ "gof" ] }, { "page": "list_cond_L", "title": "Conditions for local assessment under certain budget and cost values.", "topics": [ "list_cond_L" ] }, { "page": "list_cond_R", "title": "Conditions for regional assessment under certain budget and cost values.", "topics": [ "list_cond_R" ] }, { "page": "occumb", "title": "Model-fitting function.", "topics": [ "occumb" ] }, { "page": "occumbData", "title": "Constructor for occumbData data class.", "topics": [ "occumbData" ] }, { "page": "plot-occumbFit-method", "title": "Plot method for occumbFit class.", "topics": [ "plot,occumbFit-method" ] }, { "page": "plot-occumbGof-method", "title": "Plot method for occumbGof class.", "topics": [ "plot,occumbGof-method" ] }, { "page": "predict-occumbFit-method", "title": "Predict method for occumbFit class.", "topics": [ "predict,occumbFit-method" ] }, { "page": "summary-occumbData-method", "title": "Summary method for occumbData class.", "topics": [ "summary,occumbData-method" ] }, { "page": "summary-occumbFit-method", "title": "Summary method for occumbFit class.", "topics": [ "summary,occumbFit-method" ] } ], "_readme": "https://github.com/cran/occumb/raw/HEAD/README.md", "_rundeps": [ "backports", "checkmate", "coda", "crayon", "evaluate", "highr", "jagsUI", "knitr", "lattice", "rjags", "xfun", "yaml" ], "_sysdeps": [ { "shlib": "libjags", "package": "jags", "headers": "jags", "source": "jags", "version": "4.3.2-2.2404.0", "name": "jags", "homepage": "https://mcmc-jags.sourceforge.io", "description": "Just Another Gibbs Sampler for Bayesian MCMC - binary" }, { "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" } ], "_vignettes": [ { "source": "occumb.Rmd", "filename": "occumb.html", "title": "Introduction to occumb", "engine": "knitr::rmarkdown", "headings": [ "Prepare dataset", "Fit models", "Check posterior samples", "Predict parameter values", "Assess goodness-of-fit", "Analyze study design" ], "created": "2023-09-23 16:32:02", "modified": "2026-04-06 23:54:35", "commits": 4 }, { "source": "model_specification.Rmd", "filename": "model_specification.html", "title": "Model specification in occumb()", "engine": "knitr::rmarkdown", "headings": [ "Modeling the sequential sampling process of eDNA metabarcoding", "Covariate modeling of psi, theta, and phi", "Prior distributions", "After all, which are the relevant parameters?" ], "created": "2023-09-23 16:32:02", "modified": "2025-07-16 09:30:09", "commits": 3 }, { "source": "mcmc_engine_options.Rmd", "filename": "mcmc_engine_options.html", "title": "Options for MCMC engines in occumb()", "engine": "knitr::rmarkdown", "headings": [ "Benchmarks", "Fish dataset", "Aquatic insects dataset", "Conclusion" ], "created": "2026-04-06 23:54:35", "modified": "2026-04-06 23:54:35", "commits": 1 } ], "_score": 4.100370545117563, "_indexed": false, "_nocasepkg": "occumb", "_universes": [ "cran" ], "_indexurl": "https://fukayak.r-universe.dev/occumb", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.3.0", "date": "2026-06-14T07:14:27.000Z", "distro": "noble", "commit": "f19b843f6b713b18c7e5d53b3e0b112b0274b046", "fileid": "086873d1584eceddf62b3decd152a47246b6c9b2dda5754e99f7534bb4bfa91c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27491442576" }, { "r": "4.6.0", "os": "linux", "version": "1.3.0", "date": "2026-06-14T07:14:17.000Z", "distro": "noble", "commit": "f19b843f6b713b18c7e5d53b3e0b112b0274b046", "fileid": "7b8800176b57002247aff1060a732f2e7c9f5c7615fef77badbdfb0f3bb7fcb6", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/cran/actions/runs/27491442576" }, { "r": "4.6.0", "os": "wasm", "version": "1.3.0", "date": "2026-06-14T07:14:23.000Z", "commit": "f19b843f6b713b18c7e5d53b3e0b112b0274b046", "fileid": "892b5bb93800f86b04478363468d3b1e46466aa46f82ffff7df6273bff74cf98", "status": "success", "buildurl": "https://github.com/r-universe/cran/actions/runs/27491442576" } ] }