{
  "_id": "6aca87effe5cc25786e8af97",
  "Package": "SimReg",
  "Type": "Package",
  "Title": "Similarity Regression",
  "Version": "3.4",
  "Date": "2024-02-20",
  "Encoding": "UTF-8",
  "Author": "Daniel Greene",
  "Maintainer": "Daniel Greene <dg333@cam.ac.uk>",
  "Description": "Similarity regression, evaluating the probability of\nassociation between sets of ontological terms and binary\nresponse vector. A no-association model is compared with one in\nwhich the log odds of a true response is linked to the semantic\nsimilarity between terms and a latent characteristic\nontological profile - 'Phenotype Similarity Regression for\nIdentifying the Genetic Determinants of Rare Diseases', Greene\net al 2016 <doi:10.1016/j.ajhg.2016.01.008>.",
  "License": "GPL (>= 2)",
  "VignetteBuilder": "knitr",
  "RoxygenNote": "7.3.1",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-10 17:52:21 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://daniel-jg.r-universe.dev",
  "Date/Publication": "2024-02-22 02:29:30 UTC",
  "RemoteUrl": "https://github.com/cran/SimReg",
  "RemoteRef": "HEAD",
  "RemoteSha": "d53275aea9f925d2fae1801411859b7cdf9e777f",
  "_user": "daniel-jg",
  "_type": "src",
  "_file": "SimReg_3.4.tar.gz",
  "_fileid": "https://r2.ropensci.org/ff08101b65a438969b3a091bca9f3480b466658032b42f8ae206cf7bf4cff481",
  "_filesize": 224119,
  "_sha256": "ff08101b65a438969b3a091bca9f3480b466658032b42f8ae206cf7bf4cff481",
  "_expires": "2027-01-18T18:46:05.000Z",
  "_created": "2026-10-10T17:52:21.000Z",
  "_published": "2026-10-10T18:46:07.236Z",
  "_buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 114275665643,
      "time": 99,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11677916329"
    },
    {
      "job": 114275665638,
      "time": 132,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11678220939"
    },
    {
      "job": 114275665641,
      "time": 146,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11678385721"
    },
    {
      "job": 114275665619,
      "time": 122,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11678066164"
    },
    {
      "job": 114275665631,
      "time": 128,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11679501667"
    },
    {
      "job": 114275665599,
      "time": 266,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11677752402"
    },
    {
      "job": 114275665622,
      "time": 102,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11678651640"
    },
    {
      "job": 114275665612,
      "time": 300,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11678376094"
    },
    {
      "job": 114275006414,
      "time": 198,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11678195698"
    },
    {
      "job": 114275665533,
      "time": 97,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11677362477"
    },
    {
      "job": 114275665651,
      "time": 230,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11677567329"
    },
    {
      "job": 114275665600,
      "time": 160,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "11677896587"
    },
    {
      "job": 114275665648,
      "time": 103,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "11677492276"
    },
    {
      "job": 114275665633,
      "time": 235,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11678296133"
    },
    {
      "job": 114275665644,
      "time": 95,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11677796646"
    }
  ],
  "_upstream": "https://github.com/cran/SimReg",
  "_commit": {
    "id": "d53275aea9f925d2fae1801411859b7cdf9e777f",
    "author": "Daniel Greene <dg333@cam.ac.uk>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 3.4\n",
    "time": 1708568970
  },
  "_maintainer": {
    "name": "Daniel Greene",
    "email": "dg333@cam.ac.uk",
    "login": "daniel-jg",
    "description": "",
    "uuid": 25660818
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.0.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.11.1",
      "role": "Imports"
    },
    {
      "package": "ontologyIndex",
      "version": ">= 2.0",
      "role": "Imports"
    },
    {
      "package": "ontologySimilarity",
      "version": ">= 2.0",
      "role": "Imports"
    },
    {
      "package": "ontologyPlot",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "daniel-jg",
      "count": 8,
      "uuid": 25660818
    }
  ],
  "_userbio": {
    "uuid": 25660818,
    "type": "user",
    "name": "Daniel",
    "followers": 4
  },
  "_downloads": {
    "count": 248,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/SimReg"
  },
  "_mentions": 3,
  "_searchresults": 9,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/SimReg.html"
  ],
  "_realowner": "daniel-jg",
  "_cranurl": false,
  "_releases": [
    {
      "version": "1.1",
      "date": "2015-08-27"
    },
    {
      "version": "1.2",
      "date": "2015-09-15"
    },
    {
      "version": "1.3",
      "date": "2016-01-13"
    },
    {
      "version": "1.4",
      "date": "2016-03-06"
    },
    {
      "version": "2.1",
      "date": "2016-08-16"
    },
    {
      "version": "3.0",
      "date": "2016-10-15"
    },
    {
      "version": "3.3",
      "date": "2021-02-15"
    },
    {
      "version": "3.4",
      "date": "2024-02-21"
    }
  ],
  "_exports": [
    "get_term_marginals",
    "get_terms",
    "log_BF",
    "plot_term_marginals",
    "posterior_prediction",
    "prob_association",
    "sim_reg",
    "sum_log_probs",
    "term_marginals"
  ],
  "_help": [
    {
      "page": "SimReg-package",
      "title": "Similarity Regression Functions",
      "topics": [
        "SimReg-package",
        "SimReg"
      ]
    },
    {
      "page": "get_term_marginals",
      "title": "Calculate marginal probability of terms inclusion in 'phi' from 'sim_reg_out' object",
      "topics": [
        "get_term_marginals"
      ]
    },
    {
      "page": "get_terms",
      "title": "Get full set of terms to use in inference procedure based on similarity function arguments",
      "topics": [
        "get_terms"
      ]
    },
    {
      "page": "log_BF",
      "title": "Calculate log Bayes factor for similarity the model, 'gamma=1' and baseline model, 'gamma=0'.",
      "topics": [
        "log_BF",
        "log_BF.default",
        "log_BF.sim_reg_output"
      ]
    },
    {
      "page": "plot_term_marginals",
      "title": "Create ontological plot of marginal probabilities of terms",
      "topics": [
        "plot_term_marginals"
      ]
    },
    {
      "page": "plot.sim_reg_summary",
      "title": "Plot summary of 'sim_reg_output' object",
      "topics": [
        "plot.sim_reg_output",
        "plot.sim_reg_summary"
      ]
    },
    {
      "page": "posterior_prediction",
      "title": "Predicted probability of 'y' given 'x' conditional on association and given data.",
      "topics": [
        "posterior_prediction"
      ]
    },
    {
      "page": "print.sim_reg_output",
      "title": "Print 'sim_reg_output' object",
      "topics": [
        "print.sim_reg_output"
      ]
    },
    {
      "page": "print.sim_reg_summary",
      "title": "Print 'sim_reg_summary' object",
      "topics": [
        "print.sim_reg_summary"
      ]
    },
    {
      "page": "prob_association",
      "title": "Calculate probability of association between 'y' and 'x'",
      "topics": [
        "prob_association"
      ]
    },
    {
      "page": "sim_reg",
      "title": "Similarity regression",
      "topics": [
        "sim_reg"
      ]
    },
    {
      "page": "sum_log_probs",
      "title": "Calculate sum of log probabilities on log scale without over/under-flow",
      "topics": [
        "sum_log_probs"
      ]
    },
    {
      "page": "summary.sim_reg_output",
      "title": "Get summary of 'sim_reg_output' object",
      "topics": [
        "summary.sim_reg_output"
      ]
    },
    {
      "page": "term_marginals",
      "title": "Calculate marginal probability of terms inclusion in 'phi'",
      "topics": [
        "term_marginals"
      ]
    }
  ],
  "_rundeps": [
    "BiocGenerics",
    "generics",
    "graph",
    "ontologyIndex",
    "ontologyPlot",
    "ontologySimilarity",
    "paintmap",
    "Rcpp",
    "Rgraphviz"
  ],
  "_sysdeps": [
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "SimReg-Priors.Rmd",
      "filename": "SimReg-Priors.html",
      "title": "Prior phenotypic information",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [
        "References"
      ],
      "created": "2016-03-06 23:17:22",
      "modified": "2024-02-22 02:29:30",
      "commits": 5
    },
    {
      "source": "SimReg-Introduction.Rmd",
      "filename": "SimReg-Introduction.html",
      "title": "Similarity Regression - Introduction",
      "author": "Daniel Greene",
      "engine": "knitr::rmarkdown",
      "headings": [
        "References"
      ],
      "created": "2016-08-16 19:47:22",
      "modified": "2024-02-22 02:29:30",
      "commits": 4
    }
  ],
  "_score": 2.778151250383644,
  "_indexed": true,
  "_nocasepkg": "simreg",
  "_universes": [
    "daniel-jg"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.4",
      "date": "2026-10-10T17:54:06.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/3a261c2a0175716efe10c635a49037ac383a5eed358fed79f47deaa47f567a32",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "3.4",
      "date": "2026-10-10T17:54:25.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/d3743327a00926ae5d9b35499c1f7a7464b43e95d60923084c89e374b401c726",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "3.4",
      "date": "2026-10-10T17:54:53.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/89d69187da3ba17c1fc173fc42037de0682d31dadd483e4b46c3bef04c35c2a7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "3.4",
      "date": "2026-10-10T17:54:21.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/e55f3fd001552f7b8cac79803a2bbc93a525d97627436c9b51cd129d633e8073",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.4",
      "date": "2026-10-10T18:45:08.000Z",
      "arch": "aarch64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/11dcc19a3a382333e4f4b5495dbd0a6693ffd81ad93e0a8539d07642a2d778c4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "3.4",
      "date": "2026-10-10T17:55:55.000Z",
      "arch": "x86_64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/c3e1a0537fef3117c7d52e698f08f29893b3722de796260eca4709e57d06c06a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "3.4",
      "date": "2026-10-10T18:44:48.000Z",
      "arch": "aarch64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/d1c6bb405eac339ef4c134ae0cc26c2377222b3241c901d2d4f817b81a9c54d9",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "3.4",
      "date": "2026-10-10T17:56:19.000Z",
      "arch": "x86_64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/118eff9d108d7feb451a7c8df9f657a6621d4fd6f8a4e2f57667d8c2482f5a01",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "3.4",
      "date": "2026-10-10T17:54:17.000Z",
      "arch": "emscripten",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/33f044b5cfd6301ec3b4d63ce8557333f6492aca9ce09966498c57649e834e3a",
      "status": "success",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.4",
      "date": "2026-10-10T17:55:51.000Z",
      "arch": "aarch64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/e07dde03e738a44c139a9a9aa6326f30a65850ae7addc390d9f70aba7f379d0c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "3.4",
      "date": "2026-10-10T17:53:50.000Z",
      "arch": "x86_64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/6254433fa80707aead8c06897c5aeda6f2f538aa40fc5bafc40af25553e3858a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "3.4",
      "date": "2026-10-10T17:53:42.000Z",
      "arch": "x86_64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/a6e7bee49bd797f8598849006004489720b1c533dfe359431a03d8a1fcf6da4f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "3.4",
      "date": "2026-10-10T17:56:03.000Z",
      "arch": "aarch64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/215ac25cbd6be06a5a0654b4a8ada0771237d5d1d656e53270077789f904eb07",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "3.4",
      "date": "2026-10-10T17:53:38.000Z",
      "arch": "x86_64",
      "commit": "d53275aea9f925d2fae1801411859b7cdf9e777f",
      "fileid": "https://r2.ropensci.org/aa442951ccfa872e9f766d64f931480c753f97d71685a47a212830fb2de27793",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/daniel-jg/actions/runs/38073283326"
    }
  ]
}