{
  "_id": "6a534a519b92047c28d579bc",
  "Package": "mcstate",
  "Title": "Monte Carlo Methods for State Space Models",
  "Version": "0.9.22",
  "Authors@R": "c(person(\"Rich\", \"FitzJohn\", role = c(\"aut\", \"cre\"),\nemail = \"rich.fitzjohn@gmail.com\"),\nperson(\"Marc\", \"Baguelin\", role = \"aut\"),\nperson(\"Edward\", \"Knock\", role = \"aut\"),\nperson(\"Lilith\", \"Whittles\", role = \"aut\"),\nperson(\"John\", \"Lees\", role = \"aut\"),\nperson(\"Raphael\", \"Sonabend\", role = \"aut\"),\nperson(\"Imperial College of Science, Technology and Medicine\",\nrole = \"cph\"))",
  "Description": "Implements Monte Carlo methods for state-space models such\nas 'SIR' models in epidemiology. Particle MCMC (pmcmc) and SMC2\nmethods are planned. This package is particularly designed to\nwork with odin/dust models, but we will see how general it\nbecomes.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "Language": "en-GB",
  "URL": "https://github.com/mrc-ide/mcstate",
  "BugReports": "https://github.com/mrc-ide/mcstate/issues",
  "RoxygenNote": "7.3.1",
  "Roxygen": "list(markdown = TRUE)",
  "Remotes": [
    "mrc-ide/dust",
    "mrc-ide/odin.dust"
  ],
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake make libuv1-dev",
  "Repository": "https://mrc-ide.r-universe.dev",
  "Date/Publication": "2024-07-01 13:22:09 UTC",
  "RemoteUrl": "https://github.com/mrc-ide/mcstate",
  "RemoteRef": "master",
  "RemoteSha": "3549d64ff9b0d3aac1f9eec435093fc51f9a32cc",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-07-12 07:57:54 UTC",
    "User": "root"
  },
  "Author": "Rich FitzJohn [aut, cre],\nMarc Baguelin [aut],\nEdward Knock [aut],\nLilith Whittles [aut],\nJohn Lees [aut],\nRaphael Sonabend [aut],\nImperial College of Science, Technology and Medicine [cph]",
  "Maintainer": "Rich FitzJohn <rich.fitzjohn@gmail.com>",
  "_user": "mrc-ide",
  "_type": "src",
  "_file": "mcstate_0.9.22.tar.gz",
  "_fileid": "https://r2.ropensci.org/2e245ba1f1103c5321a82d53b5cef5b963673c80a783ac8367744c710e1deb15",
  "_filesize": 3800522,
  "_sha256": "2e245ba1f1103c5321a82d53b5cef5b963673c80a783ac8367744c710e1deb15",
  "_expires": "2026-10-20T08:03:27.000Z",
  "_created": "2026-07-12T07:57:54.000Z",
  "_published": "2026-07-12T08:03:29.689Z",
  "_jobs": [
    {
      "job": 86629598027,
      "time": 205,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8257756434"
    },
    {
      "job": 86629598029,
      "time": 235,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8257760905"
    },
    {
      "job": 86629598018,
      "time": 176,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8257752157"
    },
    {
      "job": 86629597998,
      "time": 140,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8257746668"
    },
    {
      "job": 86629242224,
      "time": 298,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8257726606"
    },
    {
      "job": 86629598010,
      "time": 108,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8257742313"
    },
    {
      "job": 86629598019,
      "time": 237,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "8257760937"
    },
    {
      "job": 86629598061,
      "time": 199,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "8257755552"
    },
    {
      "job": 86629598052,
      "time": 283,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "8257767568"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29184934918",
  "_status": "success",
  "_upstream": "https://github.com/mrc-ide/mcstate",
  "_commit": {
    "id": "3549d64ff9b0d3aac1f9eec435093fc51f9a32cc",
    "author": "Rich FitzJohn <rich.fitzjohn@gmail.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Merge pull request #241 from mrc-ide/fix-adaptive-nested\n\nFix adaptive nested",
    "time": 1719840129
  },
  "_maintainer": {
    "name": "Rich FitzJohn",
    "email": "rich.fitzjohn@gmail.com",
    "login": "richfitz",
    "mastodon": "@richfitz@fosstodon.org",
    "description": "",
    "uuid": 1558093
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R6",
      "role": "Imports"
    },
    {
      "package": "callr",
      "version": ">= 3.7.0",
      "role": "Imports"
    },
    {
      "package": "dust",
      "version": ">= 0.13.12",
      "role": "Imports"
    },
    {
      "package": "processx",
      "role": "Imports"
    },
    {
      "package": "progress",
      "version": ">= 1.2.0",
      "role": "Imports"
    },
    {
      "package": "brio",
      "role": "Suggests"
    },
    {
      "package": "coda",
      "role": "Suggests"
    },
    {
      "package": "decor",
      "role": "Suggests"
    },
    {
      "package": "fs",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "mockery",
      "role": "Suggests"
    },
    {
      "package": "mvtnorm",
      "role": "Suggests"
    },
    {
      "package": "odin.dust",
      "version": ">= 0.3.0",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "withr",
      "role": "Suggests"
    }
  ],
  "_owner": "mrc-ide",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [],
  "_tags": [],
  "_stars": 19,
  "_contributors": [
    {
      "user": "richfitz",
      "count": 812,
      "uuid": 1558093
    },
    {
      "user": "raphaels1",
      "count": 122,
      "uuid": 25639974
    },
    {
      "user": "johnlees",
      "count": 120,
      "uuid": 6331837
    },
    {
      "user": "edknock",
      "count": 106,
      "uuid": 47318334
    },
    {
      "user": "lwhittles",
      "count": 34,
      "uuid": 12626690
    },
    {
      "user": "hillalex",
      "count": 25,
      "uuid": 6736820
    },
    {
      "user": "mjomaba",
      "count": 13,
      "uuid": 6517405
    },
    {
      "user": "r-ash",
      "count": 6,
      "uuid": 39248272
    },
    {
      "user": "annecori",
      "count": 2,
      "uuid": 6973431
    },
    {
      "user": "pabloperguz",
      "count": 2,
      "uuid": 32740088
    }
  ],
  "_userbio": {
    "uuid": 25453642,
    "type": "organization",
    "name": "MRC Centre for Global Infectious Disease Analysis",
    "followers": 158,
    "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/mcstate"
  },
  "_devurl": "https://github.com/mrc-ide/mcstate",
  "_searchresults": 132,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/mcstate.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "LICENSE",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "adaptive_proposal_control",
    "array_bind",
    "array_drop",
    "array_flatten",
    "array_reshape",
    "if2",
    "if2_control",
    "if2_parameter",
    "if2_parameters",
    "if2_sample",
    "multistage_epoch",
    "multistage_parameters",
    "particle_deterministic",
    "particle_filter",
    "particle_filter_data",
    "particle_filter_initial",
    "pmcmc",
    "pmcmc_chains_cleanup",
    "pmcmc_chains_collect",
    "pmcmc_chains_prepare",
    "pmcmc_chains_run",
    "pmcmc_combine",
    "pmcmc_control",
    "pmcmc_parameter",
    "pmcmc_parameters",
    "pmcmc_parameters_nested",
    "pmcmc_predict",
    "pmcmc_sample",
    "pmcmc_thin",
    "pmcmc_varied_parameter",
    "smc2",
    "smc2_control",
    "smc2_parameter",
    "smc2_parameters"
  ],
  "_help": [
    {
      "page": "adaptive_proposal_control",
      "title": "Adaptive proposal control",
      "topics": [
        "adaptive_proposal_control"
      ]
    },
    {
      "page": "array_bind",
      "title": "Bind arrays",
      "topics": [
        "array_bind"
      ]
    },
    {
      "page": "array_drop",
      "title": "Drop specific array dimensions",
      "topics": [
        "array_drop"
      ]
    },
    {
      "page": "array_flatten",
      "title": "Flatten array dimensions",
      "topics": [
        "array_flatten"
      ]
    },
    {
      "page": "array_reshape",
      "title": "Rehape an array dimension",
      "topics": [
        "array_reshape"
      ]
    },
    {
      "page": "if2",
      "title": "Run iterated filtering (IF2 algorithm)",
      "topics": [
        "if2",
        "if2_sample"
      ]
    },
    {
      "page": "if2_control",
      "title": "Control for IF2",
      "topics": [
        "if2_control"
      ]
    },
    {
      "page": "if2_parameter",
      "title": "Describe single IF2 parameter",
      "topics": [
        "if2_parameter"
      ]
    },
    {
      "page": "if2_parameters",
      "title": "if2_parameters",
      "topics": [
        "if2_parameters"
      ]
    },
    {
      "page": "multistage_epoch",
      "title": "Multistage filter epoch",
      "topics": [
        "multistage_epoch"
      ]
    },
    {
      "page": "multistage_parameters",
      "title": "Multistage filter parameters",
      "topics": [
        "multistage_parameters"
      ]
    },
    {
      "page": "particle_deterministic",
      "title": "Deterministic particle likelihood",
      "topics": [
        "particle_deterministic"
      ]
    },
    {
      "page": "particle_deterministic_state",
      "title": "Deterministic particle state",
      "topics": [
        "particle_deterministic_state"
      ]
    },
    {
      "page": "particle_filter",
      "title": "Particle filter",
      "topics": [
        "particle_filter"
      ]
    },
    {
      "page": "particle_filter_data",
      "title": "Prepare data for use with particle filter",
      "topics": [
        "particle_filter_data"
      ]
    },
    {
      "page": "particle_filter_initial",
      "title": "Create restart initial state",
      "topics": [
        "particle_filter_initial"
      ]
    },
    {
      "page": "particle_filter_state",
      "title": "Particle filter state",
      "topics": [
        "particle_filter_state"
      ]
    },
    {
      "page": "pmcmc",
      "title": "Run a pmcmc sampler",
      "topics": [
        "pmcmc"
      ]
    },
    {
      "page": "pmcmc_chains",
      "title": "pMCMC with manual chain scheduling",
      "topics": [
        "pmcmc_chains_cleanup",
        "pmcmc_chains_collect",
        "pmcmc_chains_prepare",
        "pmcmc_chains_run"
      ]
    },
    {
      "page": "pmcmc_combine",
      "title": "Combine pmcmc samples",
      "topics": [
        "pmcmc_combine"
      ]
    },
    {
      "page": "pmcmc_control",
      "title": "Control for the pmcmc",
      "topics": [
        "pmcmc_control"
      ]
    },
    {
      "page": "pmcmc_parameter",
      "title": "Describe single pmcmc parameter",
      "topics": [
        "pmcmc_parameter"
      ]
    },
    {
      "page": "pmcmc_parameters",
      "title": "pmcmc_parameters",
      "topics": [
        "pmcmc_parameters"
      ]
    },
    {
      "page": "pmcmc_parameters_nested",
      "title": "pmcmc_parameters_nested",
      "topics": [
        "pmcmc_parameters_nested"
      ]
    },
    {
      "page": "pmcmc_predict",
      "title": "Run predictions from PMCMC",
      "topics": [
        "pmcmc_predict"
      ]
    },
    {
      "page": "pmcmc_thin",
      "title": "Thin a pmcmc chain",
      "topics": [
        "pmcmc_sample",
        "pmcmc_thin"
      ]
    },
    {
      "page": "pmcmc_varied_parameter",
      "title": "Describe varying pmcmc parameter",
      "topics": [
        "pmcmc_varied_parameter"
      ]
    },
    {
      "page": "smc2",
      "title": "Run SMC^2",
      "topics": [
        "smc2"
      ]
    },
    {
      "page": "smc2_control",
      "title": "Control for SMC2",
      "topics": [
        "smc2_control"
      ]
    },
    {
      "page": "smc2_parameter",
      "title": "Describe single pmcmc parameter",
      "topics": [
        "smc2_parameter"
      ]
    },
    {
      "page": "smc2_parameters",
      "title": "smc2_parameters",
      "topics": [
        "smc2_parameters"
      ]
    }
  ],
  "_pkglogo": "https://github.com/mrc-ide/mcstate/raw/master/man/figures/logo.png",
  "_readme": "https://github.com/mrc-ide/mcstate/raw/master/README.md",
  "_rundeps": [
    "callr",
    "cli",
    "cpp11",
    "crayon",
    "desc",
    "dust",
    "fs",
    "glue",
    "hms",
    "lifecycle",
    "otel",
    "pkgbuild",
    "pkgconfig",
    "pkgload",
    "prettyunits",
    "processx",
    "progress",
    "ps",
    "R6",
    "rlang",
    "rprojroot",
    "vctrs",
    "withr"
  ],
  "_vignettes": [
    {
      "source": "deterministic.Rmd",
      "filename": "deterministic.html",
      "title": "Deterministic models",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2021-08-09 16:17:01",
      "modified": "2022-01-28 15:30:57",
      "commits": 2
    },
    {
      "source": "continuous.Rmd",
      "filename": "continuous.html",
      "title": "Fitting a continuous-time model",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Using MCMC to infer parameters"
      ],
      "created": "2023-09-12 15:47:45",
      "modified": "2023-09-12 15:47:45",
      "commits": 1
    },
    {
      "source": "if2.Rmd",
      "filename": "if2.html",
      "title": "Inference with iterated filtering",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setting up an IF2 run",
        "Running the IF2 algorithm"
      ],
      "created": "2021-05-19 10:44:43",
      "modified": "2022-01-28 15:30:57",
      "commits": 2
    },
    {
      "source": "nested_sir_models.Rmd",
      "filename": "nested_sir_models.html",
      "title": "Nested SIR Models",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Model data",
        "Comparison, model and particle filter",
        "Nested parameters",
        "pMCMC and Visualisations"
      ],
      "created": "2021-02-24 17:22:13",
      "modified": "2022-01-28 15:30:57",
      "commits": 4
    },
    {
      "source": "parallelisation.Rmd",
      "filename": "parallelisation.html",
      "title": "Parallelisation of inference",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Within-model parallelism",
        "Between-chain parallelism",
        "Considerations"
      ],
      "created": "2020-10-26 14:15:58",
      "modified": "2022-01-28 15:30:57",
      "commits": 7
    },
    {
      "source": "restart.Rmd",
      "filename": "restart.html",
      "title": "Restarting pMCMC",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Setup",
        "All-in-one",
        "Restarting"
      ],
      "created": "2021-01-08 11:50:45",
      "modified": "2022-11-10 08:40:56",
      "commits": 7
    },
    {
      "source": "sir_models.Rmd",
      "filename": "sir_models.html",
      "title": "SIR models with odin, dust and mcstate",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Stochastic SIR model definition",
        "Inferring parameters with mcstate",
        "Model data",
        "Defining the comparison function",
        "Inferring parameters",
        "Using MCMC to infer parameters",
        "Tuning the pMCMC",
        "Running predictions",
        "Fitting to multiple datastreams"
      ],
      "created": "2020-10-26 14:15:58",
      "modified": "2022-11-10 08:40:56",
      "commits": 11
    },
    {
      "source": "kalman.Rmd",
      "filename": "kalman.html",
      "title": "Validation of SMC using a Kalman filter",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2020-10-26 14:15:58",
      "modified": "2022-11-10 08:40:56",
      "commits": 7
    }
  ],
  "_score": 7.432751287645629,
  "_indexed": true,
  "_nocasepkg": "mcstate",
  "_universes": [
    "mrc-ide",
    "richfitz"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.9.22",
      "date": "2026-07-12T07:59:57.000Z",
      "distro": "resolute",
      "commit": "3549d64ff9b0d3aac1f9eec435093fc51f9a32cc",
      "fileid": "https://r2.ropensci.org/0ab7ae44b77b0c64e5a05271a254c4e0a36710d8de9530892fe76de2d5ae190e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29184934918"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.9.22",
      "date": "2026-07-12T08:00:17.000Z",
      "distro": "resolute",
      "commit": "3549d64ff9b0d3aac1f9eec435093fc51f9a32cc",
      "fileid": "https://r2.ropensci.org/7bf5ced14488708a77052cb0c9ed7622c13d67042c55170a93b5a7ddd3fdecbd",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29184934918"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.9.22",
      "date": "2026-07-12T07:59:48.000Z",
      "commit": "3549d64ff9b0d3aac1f9eec435093fc51f9a32cc",
      "fileid": "https://r2.ropensci.org/13b2a06a719755264a5253f6a02930fd57277cc257dd4f448eb849d750b8affd",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29184934918"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.9.22",
      "date": "2026-07-12T07:59:21.000Z",
      "commit": "3549d64ff9b0d3aac1f9eec435093fc51f9a32cc",
      "fileid": "https://r2.ropensci.org/fe8d05666b8d890d487d648f1a7ebc6d563ca0e29cda472e8528bdf40c413165",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29184934918"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.9.22",
      "date": "2026-07-12T08:00:05.000Z",
      "commit": "3549d64ff9b0d3aac1f9eec435093fc51f9a32cc",
      "fileid": "https://r2.ropensci.org/ba3181bcca56ba38789c8375c26c610a957917cae744fd681cce6dcfd91280f2",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29184934918"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.9.22",
      "date": "2026-07-12T07:59:21.000Z",
      "commit": "3549d64ff9b0d3aac1f9eec435093fc51f9a32cc",
      "fileid": "https://r2.ropensci.org/90f10d8710441f9e7a3f69c0ac9562f2a9d5b93891aea4476663673d3082732b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29184934918"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.9.22",
      "date": "2026-07-12T07:59:12.000Z",
      "commit": "3549d64ff9b0d3aac1f9eec435093fc51f9a32cc",
      "fileid": "https://r2.ropensci.org/b78b9a54840960872cf5b55c0e936c7d835ce9741c04210b22e3ba17823ed26f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29184934918"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.9.22",
      "date": "2026-07-12T07:59:25.000Z",
      "commit": "3549d64ff9b0d3aac1f9eec435093fc51f9a32cc",
      "fileid": "https://r2.ropensci.org/76322c2f2102a083406f725e9fd2c3d22438f0367fa9b0a5789566c635a80d53",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/29184934918"
    }
  ]
}