{
  "_id": "6a6d7d9d4422390e5d86234e",
  "Package": "eDNAjoint",
  "Title": "Joint Modeling of Traditional and Environmental DNA Survey Data\nin a Bayesian Framework",
  "Version": "0.3.3",
  "Maintainer": "Abigail G. Keller <agkeller@berkeley.edu>",
  "Authors@R": "c(person(\"Abigail G.\", \"Keller\", role = c(\"aut\", \"cre\"), email=\"agkeller@berkeley.edu\"),\nperson(\"Ryan P.\", \"Kelly\", role = \"ctb\", email=\"rpkelly@uw.edu\"),\nperson(\"Chitra M.\", \"Saraswati\", role = \"rev\"),\nperson(\"Saras M.\", \"Windecker\", role = \"rev\"))",
  "Description": "Models integrate environmental DNA (eDNA) detection data\nand traditional survey data to jointly estimate species catch\nrate (see package vignette: <https://ednajoint.netlify.app/>).\nModels can be used with count data via traditional survey\nmethods (i.e., trapping, electrofishing, visual) and replicated\neDNA detection/nondetection data via polymerase chain reaction\n(i.e., PCR or qPCR) from multiple survey locations. Estimated\nparameters include probability of a false positive eDNA\ndetection, a site-level covariates that scale the sensitivity\nof eDNA surveys relative to traditional surveys, and gear\nscaling coefficients for traditional gear types. Models are\nimplemented with a Bayesian framework (Markov chain Monte\nCarlo) using the 'Stan' probabilistic programming language.",
  "License": "GPL-3",
  "URL": "https://github.com/ropensci/eDNAjoint,\nhttps://docs.ropensci.org/eDNAjoint/",
  "BugReports": "https://github.com/ropensci/eDNAjoint/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE, roclets = c (\"namespace\", \"rd\",\n\"srr::srr_stats_roclet\"))",
  "RoxygenNote": "7.3.2",
  "Biarch": "true",
  "SystemRequirements": "GNU make",
  "LazyData": "true",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "cmake make libicu-dev libxml2-dev",
  "Repository": "https://ropensci.r-universe.dev",
  "Date/Publication": "2025-06-20 23:47:05 UTC",
  "RemoteUrl": "https://github.com/ropensci/eDNAjoint",
  "RemoteRef": "master",
  "RemoteSha": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-31 05:42:18 UTC",
    "User": "root"
  },
  "Author": "Abigail G. Keller [aut, cre],\nRyan P. Kelly [ctb],\nChitra M. Saraswati [rev],\nSaras M. Windecker [rev]",
  "_user": "ropensci",
  "_type": "src",
  "_file": "eDNAjoint_0.3.3.tar.gz",
  "_fileid": "https://r2.ropensci.org/9a70dc4e3769a68be5214533e288d7b6efa25d811d3e803182d044c312a19a36",
  "_filesize": 2739239,
  "_sha256": "9a70dc4e3769a68be5214533e288d7b6efa25d811d3e803182d044c312a19a36",
  "_expires": "2026-11-08T06:36:55.000Z",
  "_created": "2026-07-31T05:42:18.000Z",
  "_published": "2026-08-01T05:01:17.409Z",
  "_jobs": [
    {
      "job": 91328225245,
      "time": 387,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8784317167"
    },
    {
      "job": 91328225264,
      "time": 436,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8784329219"
    },
    {
      "job": 91328225367,
      "time": 378,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8784313518"
    },
    {
      "job": 91328225350,
      "time": 473,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8784341360"
    },
    {
      "job": 91328225316,
      "time": 239,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8785062467"
    },
    {
      "job": 91328225409,
      "time": 560,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8784382328"
    },
    {
      "job": 91328225349,
      "time": 423,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8785114653"
    },
    {
      "job": 91328225358,
      "time": 880,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8784471322"
    },
    {
      "job": 91328225001,
      "time": 1277,
      "config": "pkgdown",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8784438192"
    },
    {
      "job": 91328225060,
      "time": 442,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8784207086"
    },
    {
      "job": 91328225365,
      "time": 303,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8784292320"
    },
    {
      "job": 91328225372,
      "time": 469,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8784337936"
    },
    {
      "job": 91328225014,
      "time": 548,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "8813577880"
    },
    {
      "job": 91328225011,
      "time": 442,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8813561788"
    },
    {
      "job": 91328225261,
      "time": 516,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8784351383"
    },
    {
      "job": 91328225048,
      "time": 532,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "8813575416"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247",
  "_status": "success",
  "_upstream": "https://github.com/ropensci/eDNAjoint",
  "_commit": {
    "id": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
    "author": "abigailkeller <abigail.g.keller1@gmail.com>",
    "committer": "abigailkeller <abigail.g.keller1@gmail.com>",
    "message": "updated package version\n",
    "time": 1750463225
  },
  "_maintainer": {
    "name": "Abigail G. Keller",
    "email": "agkeller@berkeley.edu",
    "login": "abigailkeller",
    "description": "PhD Candidate at UC Berkeley",
    "uuid": 62615943
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "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": ">= 2.26.23",
      "role": "LinkingTo"
    },
    {
      "package": "StanHeaders",
      "version": ">= 2.26.22",
      "role": "LinkingTo"
    },
    {
      "package": "bayestestR",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "lifecycle",
      "role": "Imports"
    },
    {
      "package": "loo",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "Imports"
    },
    {
      "package": "RcppParallel",
      "version": ">= 5.0.1",
      "role": "Imports"
    },
    {
      "package": "rlist",
      "role": "Imports"
    },
    {
      "package": "rstan",
      "version": ">= 2.26.23",
      "role": "Imports"
    },
    {
      "package": "rstantools",
      "version": ">= 2.3.1.1",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "scales",
      "role": "Imports"
    },
    {
      "package": "bayesplot",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "ropensci",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 9,
  "_contributors": [
    {
      "user": "abigailkeller",
      "count": 210,
      "uuid": 62615943
    },
    {
      "user": "andrjohns",
      "count": 1,
      "uuid": 27717896
    }
  ],
  "_userbio": {
    "uuid": 1200269,
    "type": "organization",
    "name": "rOpenSci",
    "followers": 1133,
    "description": "Tools and R Packages for Open Science"
  },
  "_downloads": {
    "count": 413,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/eDNAjoint"
  },
  "_devurl": "https://github.com/ropensci/ednajoint",
  "_pkgdown": "https://docs.ropensci.org/eDNAjoint",
  "_searchresults": 13,
  "_topics": [
    "onetbb",
    "cpp"
  ],
  "_metadata": {
    "review": {
      "id": 642,
      "status": "reviewed",
      "version": "0.1",
      "organization": "rOpenSci Software Review",
      "url": "https://github.com/ropensci/software-review/issues/642"
    },
    "ropensci_category": "stat"
  },
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/eDNAjoint.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/ropensci/ednajoint",
  "_realowner": "ropensci",
  "_cranurl": true,
  "_releases": [
    {
      "version": "0.2",
      "date": "2024-10-08"
    },
    {
      "version": "0.3",
      "date": "2025-01-17"
    },
    {
      "version": "0.3.1",
      "date": "2025-01-25"
    },
    {
      "version": "0.3.2",
      "date": "2025-03-17"
    },
    {
      "version": "0.3.3",
      "date": "2025-06-21"
    }
  ],
  "_exports": [
    "detection_calculate",
    "detection_plot",
    "joint_model",
    "joint_select",
    "joint_summarize",
    "mu_critical",
    "traditional_model"
  ],
  "_datasets": [
    {
      "name": "goby_data",
      "title": "goby_data",
      "object": "goby_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "green_crab_data",
      "title": "green_crab_data",
      "object": "green_crab_data",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "eDNAjoint-package",
      "title": "The 'eDNAjoint' package.",
      "topics": [
        "eDNAjoint-package",
        "eDNAjoint"
      ]
    },
    {
      "page": "detection_calculate",
      "title": "Calculate the survey effort necessary to detect species presence, given the species expected catch rate.",
      "topics": [
        "detection_calculate"
      ]
    },
    {
      "page": "detection_plot",
      "title": "Plot the survey effort necessary to detect species presence, given the species expected catch rate.",
      "topics": [
        "detection_plot"
      ]
    },
    {
      "page": "goby_data",
      "title": "goby_data",
      "topics": [
        "goby_data"
      ]
    },
    {
      "page": "green_crab_data",
      "title": "green_crab_data",
      "topics": [
        "green_crab_data"
      ]
    },
    {
      "page": "joint_model",
      "title": "Specify and fit joint model using count data from traditional surveys and eDNA PCR data",
      "topics": [
        "joint_model"
      ]
    },
    {
      "page": "joint_select",
      "title": "Perform model selection using leave one out cross validation of model objects",
      "topics": [
        "joint_select"
      ]
    },
    {
      "page": "joint_summarize",
      "title": "Summarize posterior distributions of model parameters.",
      "topics": [
        "joint_summarize"
      ]
    },
    {
      "page": "mu_critical",
      "title": "Calculate mu_critical",
      "topics": [
        "mu_critical"
      ]
    },
    {
      "page": "traditional_model",
      "title": "Specify and fit model using count data from traditional, non eDNA surveys",
      "topics": [
        "traditional_model"
      ]
    }
  ],
  "_pkglogo": "https://github.com/ropensci/eDNAjoint/raw/master/man/figures/logo.png",
  "_readme": "https://github.com/ropensci/eDNAjoint/raw/master/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "bayestestR",
    "BH",
    "callr",
    "checkmate",
    "cli",
    "cpp11",
    "data.table",
    "datawizard",
    "desc",
    "distributional",
    "dplyr",
    "farver",
    "generics",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "inline",
    "insight",
    "isoband",
    "jsonlite",
    "labeling",
    "lifecycle",
    "loo",
    "magrittr",
    "matrixStats",
    "numDeriv",
    "otel",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "posterior",
    "processx",
    "ps",
    "purrr",
    "QuickJSR",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppParallel",
    "rlang",
    "rlist",
    "rstan",
    "rstantools",
    "S7",
    "scales",
    "StanHeaders",
    "stringi",
    "stringr",
    "tensorA",
    "tibble",
    "tidyr",
    "tidyselect",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "XML",
    "yaml"
  ],
  "_sysdeps": [
    {
      "shlib": "libtbb",
      "package": "libtbb12",
      "headers": "libtbb-dev",
      "source": "onetbb",
      "version": "2022.3.0-2",
      "name": "onetbb",
      "homepage": "https://uxlfoundation.github.io/oneTBB/",
      "description": "parallelism library for C++ - runtime files"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_score": 3.7671558660821804,
  "_indexed": true,
  "_nocasepkg": "ednajoint",
  "_universes": [
    "ropensci",
    "abigailkeller"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.3",
      "date": "2026-07-31T05:48:03.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/0e80cd719a9164596a9877c719f116628b1ad4d7d8a45a9116719bdddd080150",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.3",
      "date": "2026-07-31T05:48:19.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/cfab9a18901e262faba6d53d02e0306c3c7d3f88efec0257b70075353e058380",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.3.3",
      "date": "2026-07-31T05:47:55.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/fe9526e527d01ae88fcb4ebcf7fe19d6edf325bd3493244d85a5b3eadd322f6b",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.3.3",
      "date": "2026-07-31T05:48:58.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/8511c67d00de43637a7c269fccece5adb3045ce1c7eaeb17f3d677c6988e1a54",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.3.3",
      "date": "2026-07-31T06:30:42.000Z",
      "arch": "aarch64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/091a1be930cb58d2696dd2e93329d2e111da206f16c43365fda281e2fe4999f0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.3.3",
      "date": "2026-07-31T05:49:57.000Z",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/265ec98790e1d48caea88dbb0ae5ccf8ccd54041710f998b1a09293badb64137",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.3.3",
      "date": "2026-07-31T06:30:58.000Z",
      "arch": "aarch64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/1790f8ccd6e8063bab94bb2686b8b54f7c69ef81532641d241602b9f6e115df5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.3.3",
      "date": "2026-07-31T05:52:21.000Z",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/d6ffb2496fe4e467562a55beb29c81dd1845388f4cbbb343dd00cff159c62a23",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.3.3",
      "date": "2026-07-31T05:48:23.000Z",
      "arch": "emscripten",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/4776ac2a8631d1419e35347d1b455cf9acdb94275bc4ff5e561b59c85db277e9",
      "status": "success",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.3.3",
      "date": "2026-07-31T05:49:12.000Z",
      "arch": "aarch64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/f22bfb5f6f9cd211e2ca1d1509e1a60bfbdd3adbb5e6d1f91b91cc40935d8601",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.3.3",
      "date": "2026-08-01T04:53:09.000Z",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/7beefc972f25cbd9479743d52f3983e45f3e4d8bb46afddfafdd31f4ca84f75e",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.3.3",
      "date": "2026-08-01T04:53:07.000Z",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/6feba78169cd155dbb129b122cd75ed183254e9f45eabd3194f3edff382697e6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.3.3",
      "date": "2026-07-31T05:49:58.000Z",
      "arch": "aarch64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/b6bc6465e1a4388591cb9e97c30d461c5d9ea12b5ebe1b69153c472cbf153651",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.3.3",
      "date": "2026-08-01T04:53:01.000Z",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "https://r2.ropensci.org/a0c16fd4c226c308e59cedc43950a306a44261b40edc62fb13a5509dcdc86288",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/30607325247"
    }
  ]
}