{
  "_id": "6a5db0749baadeef8ab53412",
  "Package": "drjacoby",
  "Type": "Package",
  "Title": "Flexible Markov Chain Monte Carlo via Reparameterization",
  "Version": "1.5.4",
  "Authors@R": "c(\nperson(\"Bob\", \"Verity\", email = \"r.verity@imperial.ac.uk\", role = c(\"aut\", \"cre\")),\nperson(\"Pete\", \"Winskill\", email = \"p.winskill@imperial.ac.uk\", role = c(\"aut\"))\n)",
  "Description": "drjacoby is an R package for performing Bayesian inference\nvia Markov chain monte carlo (MCMC). In addition to being\nhighly flexible it implements some advanced techniques that can\nimprove mixing in tricky situations.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.1",
  "BugReports": "https://github.com/mrc-ide/drjacoby/issues",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake git make libgit2-dev libicu-dev libuv1-dev\nlibssl-dev libx11-dev",
  "Repository": "https://mrc-ide.r-universe.dev",
  "Date/Publication": "2024-06-26 02:17:18 UTC",
  "RemoteUrl": "https://github.com/mrc-ide/drjacoby",
  "RemoteRef": "master",
  "RemoteSha": "edfea6339eb5a828410a0109bc9fef70c22ee210",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-20 05:16:56 UTC",
    "User": "root"
  },
  "Author": "Bob Verity [aut, cre],\nPete Winskill [aut]",
  "Maintainer": "Bob Verity <r.verity@imperial.ac.uk>",
  "_user": "mrc-ide",
  "_type": "src",
  "_file": "drjacoby_1.5.4.tar.gz",
  "_fileid": "https://r2.ropensci.org/7ffeb7d9e08930d06652a75de4cf73b657fb7cf066f16f2d458c52f5b5a58f39",
  "_filesize": 3212250,
  "_sha256": "7ffeb7d9e08930d06652a75de4cf73b657fb7cf066f16f2d458c52f5b5a58f39",
  "_expires": "2026-10-28T05:21:54.000Z",
  "_created": "2026-07-20T05:16:56.000Z",
  "_published": "2026-07-20T05:21:56.289Z",
  "_jobs": [
    {
      "job": 88277204547,
      "time": 187,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8451580114"
    },
    {
      "job": 88277204495,
      "time": 209,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8451585470"
    },
    {
      "job": 88277204515,
      "time": 238,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8451592893"
    },
    {
      "job": 88277204511,
      "time": 205,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8451584205"
    },
    {
      "job": 88277204502,
      "time": 117,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8451561533"
    },
    {
      "job": 88277204512,
      "time": 216,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8451586910"
    },
    {
      "job": 88277204499,
      "time": 180,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8451577374"
    },
    {
      "job": 88277204496,
      "time": 207,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8451584824"
    },
    {
      "job": 88276446620,
      "time": 367,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8451530932"
    },
    {
      "job": 88277204437,
      "time": 158,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8451571805"
    },
    {
      "job": 88277204466,
      "time": 199,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8451582519"
    },
    {
      "job": 88277204452,
      "time": 191,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8451580040"
    },
    {
      "job": 88277204453,
      "time": 212,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8451586231"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789",
  "_status": "success",
  "_upstream": "https://github.com/mrc-ide/drjacoby",
  "_commit": {
    "id": "edfea6339eb5a828410a0109bc9fef70c22ee210",
    "author": "bobverity <r.verity@imperial.ac.uk>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #127 from mrc-ide/develop\n\nDevelop",
    "time": 1719368238
  },
  "_maintainer": {
    "name": "Bob Verity",
    "email": "r.verity@imperial.ac.uk",
    "login": "bobverity",
    "description": "",
    "uuid": 9216594
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "coda",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "usethis",
      "role": "Imports"
    },
    {
      "package": "tools",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "cowplot",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "GGally",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "covr",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "microbenchmark",
      "role": "Suggests"
    },
    {
      "package": "gridExtra",
      "role": "Suggests"
    }
  ],
  "_owner": "mrc-ide",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 13,
  "_contributors": [
    {
      "user": "bobverity",
      "count": 208,
      "uuid": 9216594
    },
    {
      "user": "pwinskill",
      "count": 142,
      "uuid": 16702715
    }
  ],
  "_userbio": {
    "uuid": 25453642,
    "type": "organization",
    "name": "MRC Centre for Global Infectious Disease Analysis",
    "followers": 160,
    "description": "MRC Centre hosted within the Department of Infectious Disease Epidemiology at Imperial College London"
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/drjacoby"
  },
  "_devurl": "https://github.com/mrc-ide/drjacoby",
  "_searchresults": 77,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/drjacoby.html",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "check_drjacoby_loaded",
    "cpp_template",
    "define_params",
    "plot_autocorrelation",
    "plot_cor_mat",
    "plot_credible",
    "plot_density",
    "plot_mc_acceptance",
    "plot_pairs",
    "plot_rung_loglike",
    "plot_scatter",
    "plot_trace",
    "run_mcmc",
    "sample_chains"
  ],
  "_datasets": [
    {
      "name": "population_data",
      "title": "Population data.",
      "object": "population_data",
      "class": [
        "data.frame"
      ],
      "fields": [
        "pop",
        "time"
      ],
      "rows": 20,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "acf_data",
      "title": "Estimate autocorrelation",
      "topics": [
        "acf_data"
      ]
    },
    {
      "page": "check_drjacoby_loaded",
      "title": "Check that drjacoby package has loaded successfully",
      "topics": [
        "check_drjacoby_loaded"
      ]
    },
    {
      "page": "cpp_template",
      "title": "Create template for cpp",
      "topics": [
        "cpp_template"
      ]
    },
    {
      "page": "define_params",
      "title": "Define parameters dataframe",
      "topics": [
        "define_params"
      ]
    },
    {
      "page": "drjacoby",
      "title": "Flexible Markov Chain Monte Carlo via Reparameterization",
      "topics": [
        "drjacoby"
      ]
    },
    {
      "page": "gelman_rubin",
      "title": "Gelman-Rubin statistic",
      "topics": [
        "gelman_rubin"
      ]
    },
    {
      "page": "plot_autocorrelation",
      "title": "Plot autocorrelation",
      "topics": [
        "plot_autocorrelation"
      ]
    },
    {
      "page": "plot_cor_mat",
      "title": "Plot posterior correlation matrix",
      "topics": [
        "plot_cor_mat"
      ]
    },
    {
      "page": "plot_credible",
      "title": "Plot 95% credible intervals",
      "topics": [
        "plot_credible"
      ]
    },
    {
      "page": "plot_density",
      "title": "Produce density plots",
      "topics": [
        "plot_density"
      ]
    },
    {
      "page": "plot_mc_acceptance",
      "title": "Plot Metropolis coupling acceptance rates",
      "topics": [
        "plot_mc_acceptance"
      ]
    },
    {
      "page": "plot_pairs",
      "title": "Produce scatterplots between multiple parameters",
      "topics": [
        "plot_pairs"
      ]
    },
    {
      "page": "plot_rung_loglike",
      "title": "Plot loglikelihood 95% credible intervals",
      "topics": [
        "plot_rung_loglike"
      ]
    },
    {
      "page": "plot_scatter",
      "title": "Produce bivariate scatterplot",
      "topics": [
        "plot_scatter"
      ]
    },
    {
      "page": "plot_trace",
      "title": "Plot parameter trace",
      "topics": [
        "plot_trace"
      ]
    },
    {
      "page": "population_data",
      "title": "Population data.",
      "topics": [
        "population_data"
      ]
    },
    {
      "page": "run_mcmc",
      "title": "Run drjacoby MCMC",
      "topics": [
        "run_mcmc"
      ]
    },
    {
      "page": "sample_chains",
      "title": "Sample posterior draws from all available chains",
      "topics": [
        "sample_chains"
      ]
    }
  ],
  "_readme": "https://github.com/mrc-ide/drjacoby/raw/master/README.md",
  "_rundeps": [
    "askpass",
    "cli",
    "clipr",
    "coda",
    "cowplot",
    "cpp11",
    "crayon",
    "credentials",
    "curl",
    "desc",
    "dplyr",
    "farver",
    "forcats",
    "fs",
    "generics",
    "gert",
    "GGally",
    "ggplot2",
    "ggstats",
    "gitcreds",
    "glue",
    "gtable",
    "hms",
    "httr2",
    "ini",
    "isoband",
    "jsonlite",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "openssl",
    "patchwork",
    "pillar",
    "pkgconfig",
    "prettyunits",
    "progress",
    "purrr",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "rlang",
    "rprojroot",
    "rstudioapi",
    "S7",
    "scales",
    "stringi",
    "stringr",
    "sys",
    "tibble",
    "tidyr",
    "tidyselect",
    "usethis",
    "utf8",
    "vctrs",
    "viridisLite",
    "whisker",
    "withr",
    "yaml",
    "zip"
  ],
  "_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": "example.Rmd",
      "filename": "example.html",
      "title": "Basic Example",
      "author": "Bob Verity and Pete Winskill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup",
        "Running the MCMC",
        "Exploring outputs and checking MCMC performance",
        "Using C++ functions"
      ],
      "created": "2019-05-03 12:09:09",
      "modified": "2024-06-26 02:17:18",
      "commits": 21
    },
    {
      "source": "checks_double_well.Rmd",
      "filename": "checks_double_well.html",
      "title": "Double well",
      "author": "Bob Verity and Pete Winskill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Model",
        "Single temperature rung (no Metropolis coupling)",
        "Multiple temperature rungs"
      ],
      "created": "2021-09-08 14:42:41",
      "modified": "2024-06-26 02:17:18",
      "commits": 3
    },
    {
      "source": "getting_model_fits.Rmd",
      "filename": "getting_model_fits.html",
      "title": "Getting Model Fits",
      "author": "Bob Verity and Pete Winskill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "A simple model of population growth"
      ],
      "created": "2022-02-10 09:37:00",
      "modified": "2024-06-26 02:17:18",
      "commits": 2
    },
    {
      "source": "installation.Rmd",
      "filename": "installation.html",
      "title": "Installing drjacoby",
      "author": "Bob Verity and Pete Winskill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installing Rcpp",
        "Installing and loading drjacoby"
      ],
      "created": "2019-05-02 13:45:52",
      "modified": "2024-06-26 02:17:18",
      "commits": 6
    },
    {
      "source": "checks_multilevel_blocks.Rmd",
      "filename": "checks_multilevel_blocks.html",
      "title": "Multilevel example with blocks",
      "author": "Bob Verity and Pete Winskill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Model",
        "MCMC",
        "Plots"
      ],
      "created": "2021-09-08 14:42:41",
      "modified": "2021-09-08 14:42:41",
      "commits": 1
    },
    {
      "source": "checks_normal_model.Rmd",
      "filename": "checks_normal_model.html",
      "title": "Normal model",
      "author": "Bob Verity and Pete Winskill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Model",
        "MCMC",
        "Posterior plots"
      ],
      "created": "2021-09-08 14:42:41",
      "modified": "2021-09-08 14:42:41",
      "commits": 1
    },
    {
      "source": "metropolis_coupling.Rmd",
      "filename": "metropolis_coupling.html",
      "title": "Parallel Tempering",
      "author": "Bob Verity and Pete Winskill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup",
        "Running the MCMC",
        "How many rungs to use?"
      ],
      "created": "2019-05-22 09:00:19",
      "modified": "2024-06-26 02:17:18",
      "commits": 14
    },
    {
      "source": "checks_return_prior.Rmd",
      "filename": "checks_return_prior.html",
      "title": "Return prior",
      "author": "Bob Verity and Pete Winskill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Model",
        "Run MCMC",
        "Plots"
      ],
      "created": "2021-09-08 14:42:41",
      "modified": "2021-09-08 14:42:41",
      "commits": 1
    },
    {
      "source": "parallel.Rmd",
      "filename": "parallel.html",
      "title": "Running in Parallel",
      "author": "Bob Verity and Pete Winskill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup",
        "Running multiple chains",
        "Running multiple chains using C++ log likelihood or log prior functions"
      ],
      "created": "2019-05-22 16:36:16",
      "modified": "2024-06-26 02:17:18",
      "commits": 11
    },
    {
      "source": "blocks.Rmd",
      "filename": "blocks.html",
      "title": "Using Likelihood Blocks",
      "author": "Bob Verity and Pete Winskill",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Problem motivation",
        "Defining blocks",
        "The Likelihood"
      ],
      "created": "2021-01-08 15:30:58",
      "modified": "2022-02-10 09:37:00",
      "commits": 4
    }
  ],
  "_score": 5.699404081815338,
  "_indexed": true,
  "_nocasepkg": "drjacoby",
  "_universes": [
    "mrc-ide",
    "bobverity"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5.4",
      "date": "2026-07-20T05:19:44.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/6bccf7b4ebceb7e4145b804902b768ed6387175f3ec63f73a6eb45383fd3cef7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.5.4",
      "date": "2026-07-20T05:20:06.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/f87f749ff7f0dedd3920e4394679ed45c19042cd1a0dd0957573ec19c1a3f40e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.5.4",
      "date": "2026-07-20T05:20:28.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/c079e4c0dab62436e1794fbf7f73deb86075e2971b918c203128998cac8b8a83",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.5.4",
      "date": "2026-07-20T05:19:45.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/c5c5a4722254dc6a7bad5fa0e1f5935541f33199de11a790a0a472cb41da2db1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5.4",
      "date": "2026-07-20T05:18:40.000Z",
      "arch": "aarch64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/24526e88b3b419adbd6ac252b482328b086915c8dfbab23972b34e941ba72cf3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.5.4",
      "date": "2026-07-20T05:19:37.000Z",
      "arch": "x86_64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/f0f1a5296abf2f09c53579e4f5ce20d40570bbb627d141b568d30afaffd1619f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.5.4",
      "date": "2026-07-20T05:18:58.000Z",
      "arch": "aarch64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/135a11bd507e80b817652ec60aed16eb121ee9acecbf22a1b3b4cd3c4c4cd6d5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.5.4",
      "date": "2026-07-20T05:19:26.000Z",
      "arch": "x86_64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/126f1f3c074c166cb7dacdca96602238154abd3fdfe88145e54f8f97186d1ba1",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.5.4",
      "date": "2026-07-20T05:19:52.000Z",
      "arch": "emscripten",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/0851b45eade2dcd0541ccd78ce62cb6cd550eb02813644e266e377993a5a5053",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.5.4",
      "date": "2026-07-20T05:18:36.000Z",
      "arch": "x86_64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/ed65d7ab4e94a1f77c649e7019249aa50ec745d3111f814bc51f8eb6f2eec344",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.5.4",
      "date": "2026-07-20T05:18:25.000Z",
      "arch": "x86_64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/50e616226296a45a428eb4b9fae26f4022f0ca4be4730225a9653f93d66f91d7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.5.4",
      "date": "2026-07-20T05:18:37.000Z",
      "arch": "x86_64",
      "commit": "edfea6339eb5a828410a0109bc9fef70c22ee210",
      "fileid": "https://r2.ropensci.org/61165145a3c6665e166e87500b72dc16634e52628fb7ba22802d78ae7c5ad6cc",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29718532789"
    }
  ]
}