{
  "_id": "6a154c03acfb0bcc41d59015",
  "Package": "gjam",
  "Type": "Package",
  "Title": "Generalized Joint Attribute Modeling",
  "Version": "2.7",
  "Date": "2025-10-27",
  "Authors@R": "c(person(given = c(\"James\", \"S.\"),\nfamily = \"Clark\",\nrole = c(\"aut\", \"cre\"),\nemail = \"jimclark@duke.edu\"),\nperson(given = \"Daniel\",\nfamily = \"Taylor-Rodriquez\",\nrole = \"aut\"))",
  "Maintainer": "James S. Clark <jimclark@duke.edu>",
  "Description": "Analyzes joint attribute data (e.g., species abundance)\nthat are combinations of continuous and discrete data with\nGibbs sampling.  Full model and computation details are\ndescribed in Clark et al. (2018) <doi:10.1002/ecm.1241>.",
  "License": "GPL (>= 2)",
  "VignetteBuilder": "knitr",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-26 07:26:41 UTC",
    "User": "root"
  },
  "Author": "James S. Clark [aut, cre], Daniel Taylor-Rodriquez [aut]",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2025-10-28 20:40:02 UTC",
  "RemoteUrl": "https://github.com/cran/gjam",
  "RemoteRef": "HEAD",
  "RemoteSha": "d19879275840c929ddd168ca262793699a27c6e2",
  "MD5sum": "23a0a9687efd187aac774e45cc58b632",
  "_user": "cran",
  "_type": "src",
  "_file": "gjam_2.7.tar.gz",
  "_fileid": "3a0d0a9ce3a37870164c26490dfc9d8548e29b2fe13434806a21518f93477888",
  "_filesize": 564500,
  "_sha256": "3a0d0a9ce3a37870164c26490dfc9d8548e29b2fe13434806a21518f93477888",
  "_created": "2026-05-26T07:26:41.000Z",
  "_published": "2026-05-26T07:30:11.105Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77827076010,
      "time": 144,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7211252671"
    },
    {
      "job": 77827076031,
      "time": 124,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7211246397"
    },
    {
      "job": 77827076048,
      "time": 141,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211251803"
    },
    {
      "job": 77827076002,
      "time": 145,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211253263"
    },
    {
      "job": 77826577768,
      "time": 205,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211207680"
    },
    {
      "job": 77827075977,
      "time": 108,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7211241127"
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/26438271338",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/gjam",
  "_commit": {
    "id": "d19879275840c929ddd168ca262793699a27c6e2",
    "author": "James S. Clark <jimclark@duke.edu>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.7\n",
    "time": 1761684002
  },
  "_maintainer": {
    "name": "James S. Clark",
    "email": "jimclark@duke.edu",
    "login": "jimclarkatduke",
    "description": "Nicholas Professor\nNicholas School of the Environment\nDepartment of Statistical Science\n",
    "uuid": 16857645
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 2.10",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.11.5",
      "role": "Imports"
    },
    {
      "package": "MASS",
      "role": "Imports"
    },
    {
      "package": "RANN",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "2.7",
      "date": "2025-10-28"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "jimclarkatduke",
      "count": 34,
      "uuid": 16857645
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 277,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/gjam"
  },
  "_mentions": 1,
  "_searchresults": 144,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/gjam.html",
    "manual.pdf"
  ],
  "_realowner": "jimclarkatduke",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.0",
      "date": "2016-01-04"
    },
    {
      "version": "2.0",
      "date": "2016-10-07"
    },
    {
      "version": "2.1",
      "date": "2016-11-29"
    },
    {
      "version": "2.1.1",
      "date": "2016-12-14"
    },
    {
      "version": "2.1.3",
      "date": "2017-04-24"
    },
    {
      "version": "2.1.4",
      "date": "2017-05-11"
    },
    {
      "version": "2.1.5",
      "date": "2017-07-31"
    },
    {
      "version": "2.1.6",
      "date": "2017-09-11"
    },
    {
      "version": "2.1.7",
      "date": "2017-12-22"
    },
    {
      "version": "2.1.8",
      "date": "2018-01-04"
    },
    {
      "version": "2.1.9",
      "date": "2018-02-27"
    },
    {
      "version": "2.2.0",
      "date": "2018-03-28"
    },
    {
      "version": "2.2.1",
      "date": "2018-03-29"
    },
    {
      "version": "2.2.2",
      "date": "2018-05-22"
    },
    {
      "version": "2.2.3",
      "date": "2018-05-30"
    },
    {
      "version": "2.2.4",
      "date": "2018-06-02"
    },
    {
      "version": "2.2.5",
      "date": "2018-08-02"
    },
    {
      "version": "2.2.6",
      "date": "2018-09-22"
    },
    {
      "version": "2.2.7",
      "date": "2019-04-17"
    },
    {
      "version": "2.3",
      "date": "2020-03-02"
    },
    {
      "version": "2.3.1",
      "date": "2020-03-18"
    },
    {
      "version": "2.3.2",
      "date": "2020-06-15"
    },
    {
      "version": "2.3.4",
      "date": "2021-02-10"
    },
    {
      "version": "2.3.5",
      "date": "2021-03-29"
    },
    {
      "version": "2.3.6",
      "date": "2021-04-11"
    },
    {
      "version": "2.3.7",
      "date": "2021-05-24"
    },
    {
      "version": "2.3.8",
      "date": "2021-07-06"
    },
    {
      "version": "2.3.9",
      "date": "2021-07-14"
    },
    {
      "version": "2.5",
      "date": "2021-10-12"
    },
    {
      "version": "2.5.1",
      "date": "2022-01-09"
    },
    {
      "version": "2.5.2",
      "date": "2022-02-15"
    },
    {
      "version": "2.6",
      "date": "2022-04-15"
    },
    {
      "version": "2.6.2",
      "date": "2022-05-23"
    },
    {
      "version": "2.7",
      "date": "2025-10-28"
    }
  ],
  "_exports": [
    "gjam",
    "gjamCensorY",
    "gjamConditionalParameters",
    "gjamDeZero",
    "gjamFillMissingTimes",
    "gjamIIE",
    "gjamIIEplot",
    "gjamOrdination",
    "gjamPlot",
    "gjamPoints2Grid",
    "gjamPredict",
    "gjamPriorTemplate",
    "gjamReZero",
    "gjamSensitivity",
    "gjamSimData",
    "gjamSpec2Trait",
    "gjamTrimY"
  ],
  "_help": [
    {
      "page": "gjam-package",
      "title": "Generalized Joint Attribute Modeling",
      "topics": [
        "gjam-package",
        "GJAM"
      ]
    },
    {
      "page": "gjam",
      "title": "Generalized Joint Attribute Modeling",
      "topics": [
        "gjam",
        "print.gjam",
        "summary.gjam"
      ]
    },
    {
      "page": "gjamCensorY",
      "title": "Censor gjam response data",
      "topics": [
        "gjamCensorY"
      ]
    },
    {
      "page": "gjamConditionalParameters",
      "title": "Parameters for gjam conditional prediction",
      "topics": [
        "gjamConditionalParameters"
      ]
    },
    {
      "page": "gjamDeZero",
      "title": "Compress (de-zero) gjam data",
      "topics": [
        "gjamDeZero"
      ]
    },
    {
      "page": "gjamFillMissingTimes",
      "title": "Fill out data for time series (state-space) gjam",
      "topics": [
        "gjamFillMissingTimes"
      ]
    },
    {
      "page": "gjamIIE",
      "title": "Indirect effects and interactions for gjam data",
      "topics": [
        "gjamIIE"
      ]
    },
    {
      "page": "gjamIIEplot",
      "title": "Plots indirect effects and interactions for gjam data",
      "topics": [
        "gjamIIEplot"
      ]
    },
    {
      "page": "gjamOrdination",
      "title": "Ordinate gjam data",
      "topics": [
        "gjamOrdination"
      ]
    },
    {
      "page": "gjamPlot",
      "title": "Plot gjam analysis",
      "topics": [
        "gjamPlot"
      ]
    },
    {
      "page": "gjamPoints2Grid",
      "title": "Incidence point pattern to grid counts",
      "topics": [
        "gjamPoints2Grid"
      ]
    },
    {
      "page": "gjamPredict",
      "title": "Predict gjam data",
      "topics": [
        "gjamPredict"
      ]
    },
    {
      "page": "gjamPriorTemplate",
      "title": "Prior coefficients for gjam analysis",
      "topics": [
        "gjamPriorTemplate"
      ]
    },
    {
      "page": "gjamReZero",
      "title": "Expand (re-zero) gjam data",
      "topics": [
        "gjamReZero"
      ]
    },
    {
      "page": "gjamSensitivity",
      "title": "Sensitivity coefficients for gjam",
      "topics": [
        "gjamSensitivity"
      ]
    },
    {
      "page": "gjamSimData",
      "title": "Simulated data for gjam analysis",
      "topics": [
        "gjamSimData"
      ]
    },
    {
      "page": "gjamSpec2Trait",
      "title": "Ecological traits for gjam analysis",
      "topics": [
        "gjamSpec2Trait"
      ]
    },
    {
      "page": "gjamTrimY",
      "title": "Trim gjam response data",
      "topics": [
        "gjamTrimY"
      ]
    }
  ],
  "_rundeps": [
    "MASS",
    "RANN",
    "Rcpp",
    "RcppArmadillo"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.26+ds-1ubuntu0.1",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "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"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "14.2.0-4ubuntu2~24.04.1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_vignettes": [
    {
      "source": "gjamVignette.Rmd",
      "filename": "gjamVignette.html",
      "title": "Generalized joint attribute modeling - gjam",
      "author": "James S. Clark",
      "engine": "knitr::rmarkdown",
      "headings": [
        "<span style=\"color:darkgreen\">overview</span>",
        "<span style=\"color:teal\">model summary</span>",
        "<span style=\"color:teal\">data types</span>",
        "<span style=\"color:teal\">effort and weight of discrete data</span>",
        "<span style=\"color:darkgreen\">using gjam</span>",
        "<span style=\"color:teal\">simulated data</span>",
        "<span style=\"color:teal\">my data</span>",
        "<span style=\"color:darkgreen\">sensitivity to predictors</span>",
        "<span style=\"color:darkgreen\">plotting output</span>",
        "<span style=\"color:darkgreen\">flexibility in gjam</span>",
        "<span style=\"color:teal\">heterogeneous effort</span>",
        "<span style=\"color:teal\">specifying censored intervals</span>",
        "<span style=\"color:teal\">prior distribution on coefficients</span>",
        "<span style=\"color:teal\">species-factor levels that do not occur</span>",
        "<span style=\"color:teal\">sample effort in count data</span>",
        "<span style=\"color:teal\">sample effort in composition data</span>",
        "<span style=\"color:teal\">the partition in ordinal data</span>",
        "<span style=\"color:teal\">categorical data</span>",
        "<span style=\"color:teal\">combinations of data types</span>",
        "<span style=\"color:teal\">random effects</span>",
        "<span style=\"color:teal\">missing data, out-of-sample prediction</span>",
        "<span style=\"color:teal\">prediction with heterogenous effort</span>",
        "<span style=\"color:teal\">conditional prediction</span>",
        "<span style=\"color:teal\">conditional parameters</span>",
        "<span style=\"color:teal\">presence-only data with effort</span>",
        "<span style=\"color:darkgreen\">dimension reduction</span>",
        "<span style=\"color:teal\">big-S composition data: fungal endophytes</span>",
        "<span style=\"color:teal\">interactions and indirect effects</span>",
        "<span style=\"color:darkgreen\">joint trait modeling</span>",
        "<span style=\"color:teal\">trait response model (TRM)</span>",
        "<span style=\"color:brown\">input data</span>",
        "<span style=\"color:brown\">traits by species</span>",
        "<span style=\"color:brown\">factors in this example</span>",
        "<span style=\"color:brown\">TRM analysis</span>",
        "<span style=\"color:brown\">interactions and indirect effects</span>",
        "<span style=\"color:teal\">predictive trait model (PTM)</span>",
        "<span style=\"color:brown\">start with species abundance</span>",
        "<span style=\"color:brown\">trouble shooting in PTM</span>",
        "<span style=\"color:darkgreen\">selecting variables</span>",
        "<span style=\"color:darkgreen\">trouble shooting</span>",
        "<span style=\"color:darkgreen\">reference notes</span>",
        "<span style=\"color:teal\">more on parameter dimensions</span>",
        "<span style=\"color:teal\">more on factors in $\\mathbf{X}$</span>",
        "<span style=\"color:darkgreen\">algorithm summary</span>",
        "<span style=\"color:darkgreen\">acknowledgements</span>",
        "<span style=\"color:darkgreen\">references</span>"
      ],
      "created": "2016-01-04 23:10:32",
      "modified": "2025-10-28 20:40:02",
      "commits": 31
    }
  ],
  "_score": 3.1583624920952498,
  "_indexed": false,
  "_nocasepkg": "gjam",
  "_universes": [
    "cran"
  ],
  "_indexurl": "https://jimclarkatduke.r-universe.dev/gjam",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.7",
      "date": "2026-05-26T07:28:56.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "d19879275840c929ddd168ca262793699a27c6e2",
      "fileid": "8aa4779913517bc5a21fe72a34478d1b6be59c8f0073a2a208c86508739a1344",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26438271338"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.7",
      "date": "2026-05-26T07:28:39.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "d19879275840c929ddd168ca262793699a27c6e2",
      "fileid": "45c8361f2f118540eecb2b024648948bf75300cd580c484d5052e8ddcc0e1c69",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26438271338"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.7",
      "date": "2026-05-26T07:28:52.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "d19879275840c929ddd168ca262793699a27c6e2",
      "fileid": "973fea2ee83e26aef9f19c79fd79b1af61f4de6b1edc975db6264eff3954c254",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26438271338"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.7",
      "date": "2026-05-26T07:28:56.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "d19879275840c929ddd168ca262793699a27c6e2",
      "fileid": "4b8b99c1469f239daf210359bbe9ff775abbd97b304e5139315f144e916f01bf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26438271338"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.7",
      "date": "2026-05-26T07:29:00.000Z",
      "arch": "emscripten",
      "commit": "d19879275840c929ddd168ca262793699a27c6e2",
      "fileid": "740f4f68424410066f1d4cf3c062681a98c2ae8b90fffa584be6d32c8578eea1",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/26438271338"
    }
  ]
}