{
  "_id": "6a06f1e87b0ee7a561a728b2",
  "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": "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": "2026-05-15 09:52:11 UTC",
    "User": "root"
  },
  "Author": "Abigail G. Keller [aut, cre],\nRyan P. Kelly [ctb],\nChitra M. Saraswati [rev],\nSaras M. Windecker [rev]",
  "MD5sum": "aba012391af1b860198c9b213128cbba",
  "_user": "ropensci",
  "_type": "src",
  "_file": "eDNAjoint_0.3.3.tar.gz",
  "_fileid": "e7d589724819de9ccc2ec30bda6c59b2ff9fe6e4a907bd89700dc0c03b406e3f",
  "_filesize": 2740609,
  "_sha256": "e7d589724819de9ccc2ec30bda6c59b2ff9fe6e4a907bd89700dc0c03b406e3f",
  "_created": "2026-05-15T09:52:11.000Z",
  "_published": "2026-05-15T10:14:00.392Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 76158342103,
      "time": 422,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7014647867"
    },
    {
      "job": 76158342046,
      "time": 427,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7014650948"
    },
    {
      "job": 76158342057,
      "time": 427,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014648901"
    },
    {
      "job": 76158342089,
      "time": 434,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014651101"
    },
    {
      "job": 76158342068,
      "time": 279,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7014667275"
    },
    {
      "job": 76158342099,
      "time": 458,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7014672939"
    },
    {
      "job": 76158342073,
      "time": 269,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014826307"
    },
    {
      "job": 76158342036,
      "time": 656,
      "config": "macos-release-x86_64",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014720582"
    },
    {
      "job": 76157285435,
      "time": 1271,
      "config": "pkgdown",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7014758652"
    },
    {
      "job": 76157285374,
      "time": 451,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7014521518"
    },
    {
      "job": 76158342030,
      "time": 182,
      "config": "wasm-release",
      "r": "4.5.1",
      "check": "FAIL",
      "artifact": ""
    },
    {
      "job": 76158342077,
      "time": 514,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "7014673865"
    },
    {
      "job": 76158342060,
      "time": 574,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "7014690908"
    },
    {
      "job": 76158342094,
      "time": 530,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "NOTE",
      "artifact": "7014679315"
    }
  ],
  "_buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_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",
    "uuid": 62615943
  },
  "_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": [
    {
      "week": "2025-24",
      "n": 9
    },
    {
      "week": "2025-25",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 8,
  "_contributors": [
    {
      "user": "abigailkeller",
      "count": 210,
      "uuid": 62615943
    },
    {
      "user": "andrjohns",
      "count": 1,
      "uuid": 27717896
    }
  ],
  "_userbio": {
    "uuid": 1200269,
    "type": "organization",
    "name": "rOpenSci",
    "description": "Tools and R Packages for Open Science"
  },
  "_downloads": {
    "count": 225,
    "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": [
    "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": "4.6.0",
  "_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",
    "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": "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": 4.017033339298781,
  "_indexed": true,
  "_nocasepkg": "ednajoint",
  "_universes": [
    "ropensci",
    "abigailkeller"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.3",
      "date": "2026-05-15T09:58:05.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "83e911613e2af98b878441b9098e5d88eb86e01fc0d37b4931de8ef23f9bd844",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.3.3",
      "date": "2026-05-15T09:58:20.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "a140c8542fe69ed912ffff1a6b829ffc9d74b3f9dc0ca58892cc7c67c9b4685f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.3.3",
      "date": "2026-05-15T09:58:05.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "6d3f00d7b6c6a5ef01b4d43e9b272c92df65f1e5a07a31c30cdd7257f28695a5",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.3.3",
      "date": "2026-05-15T09:58:20.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "4302febcc073ca9819718789fed9ece1e07c270d6150a646fd4ba02f5bcc52db",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.3.3",
      "date": "2026-05-15T10:00:57.000Z",
      "arch": "aarch64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "9795dc34488ed7ec4087a40f7ba905da11aabf8a4d51b100fe26768d2b3ef6ed",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.3.3",
      "date": "2026-05-15T09:58:40.000Z",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "e844117ed0a5b148a363b937521d8742131d4dec3595d1d269ad628bf58c94cb",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.3.3",
      "date": "2026-05-15T10:10:24.000Z",
      "arch": "aarch64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "217c056fbd53da9f884c61901c82f93a2b73625b73d25a6861b79a0f06038f7a",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.3.3",
      "date": "2026-05-15T09:59:30.000Z",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "75fa5623a1a32b9faa9e6d36a8e3eef115ec06242e69b0be6c07cc2f9650bee6",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.3.3",
      "date": "2026-05-15T09:57:10.000Z",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "48f4274cb3a6ca564ad4216362b8de334ae7667b0b9af2d0759d27d3831e5cd0",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.3.3",
      "date": "2026-05-15T09:57:27.000Z",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "d53c711af718b30ab95a05f49a9c9eeda749f2c69383011968119086d6c19851",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.3.3",
      "date": "2026-05-15T09:57:32.000Z",
      "arch": "x86_64",
      "commit": "e86c3017c65eb281c7372868da18e0eebd45b3d3",
      "fileid": "05505ffcb1a048b89b7ec2d916ec33ba26bd516efd672efaecd1354ab97fe3be",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/ropensci/actions/runs/25911421382"
    }
  ]
}