{
  "_id": "6a1f293db401979e73423ea4",
  "Package": "rts2",
  "Title": "Real-Time Disease Surveillance",
  "Version": "1.0.2",
  "Date": "2026-04-25",
  "Authors@R": "person(given = \"Sam\",\nfamily = \"Watson\",\nrole = c(\"aut\", \"cre\"),\nemail = \"s.i.watson@bham.ac.uk\",\ncomment = c(ORCID = \"0000-0002-8972-769X\"))",
  "Description": "Supports modelling real-time case data to facilitate the\nreal-time surveillance of infectious diseases and other point\nphenomena. The package provides automated computational grid\ngeneration over an area of interest with methods to map\ncovariates between geographies, model fitting including\nspatially aggregated case counts, and predictions and\nvisualisation. Both Bayesian and maximum likelihood methods are\nprovided. Log-Gaussian Cox Processes are described by Diggle et\nal. (2013) <doi:10.1214/13-STS441> and we provide both the\nlow-rank approximation for Gaussian processes described by\nSolin and Särkkä (2020) <doi:10.1007/s11222-019-09886-w> and\nRiutort-Mayol et al (2023) <doi:10.1007/s11222-022-10167-2> and\nthe nearest neighbour Gaussian process described by Datta et al\n(2016) <doi:10.1080/01621459.2015.1044091>.",
  "License": "CC BY-SA 4.0",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.3",
  "Biarch": "true",
  "SystemRequirements": "GNU make",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-05-15 09:56:03 UTC",
    "User": "root"
  },
  "Author": "Sam Watson [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8972-769X>)",
  "Maintainer": "Sam Watson <s.i.watson@bham.ac.uk>",
  "Config/pak/sysreqs": "make",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2026-04-30 18:49:32 UTC",
  "RemoteUrl": "https://github.com/cran/rts2",
  "RemoteRef": "HEAD",
  "RemoteSha": "71f560d224226a8f315f535ec177bb47b9b00840",
  "MD5sum": "a285bb08f272370f5fbc900d790e10d0",
  "_user": "cran",
  "_type": "src",
  "_file": "rts2_1.0.2.tar.gz",
  "_fileid": "f2ff9c8b98378462467eef5e2daf73a17e4e5fc6e987ac6a2e242d7904f79b0c",
  "_filesize": 1366334,
  "_sha256": "f2ff9c8b98378462467eef5e2daf73a17e4e5fc6e987ac6a2e242d7904f79b0c",
  "_created": "2026-05-15T09:56:03.000Z",
  "_published": "2026-06-02T19:04:29.616Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79149671652,
      "time": 486,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7030642973"
    },
    {
      "job": 79149670771,
      "time": 479,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7030642238"
    },
    {
      "job": 79149671187,
      "time": 471,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7014721274"
    },
    {
      "job": 79149671007,
      "time": 485,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7014726700"
    },
    {
      "job": 79149670710,
      "time": 533,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7014584697"
    },
    {
      "job": 79149670335,
      "time": 254,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "FAIL",
      "artifact": ""
    }
  ],
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/25911497873",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cran/rts2",
  "_commit": {
    "id": "71f560d224226a8f315f535ec177bb47b9b00840",
    "author": "Sam Watson <s.i.watson@bham.ac.uk>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 1.0.2\n",
    "time": 1777574972
  },
  "_maintainer": {
    "name": "Sam Watson",
    "email": "s.i.watson@bham.ac.uk",
    "login": "samueliwatson",
    "uuid": 69966855,
    "orcid": "0000-0002-8972-769X"
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.5.0",
      "role": "Depends"
    },
    {
      "package": "sf",
      "version": ">= 1.0-14",
      "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": ">= 2.30.0",
      "role": "LinkingTo"
    },
    {
      "package": "StanHeaders",
      "version": ">= 2.32.0",
      "role": "LinkingTo"
    },
    {
      "package": "glmmrBase",
      "version": ">= 1.3.0",
      "role": "LinkingTo"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "R6",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "version": ">= 0.12.0",
      "role": "Imports"
    },
    {
      "package": "RcppParallel",
      "version": ">= 5.0.1",
      "role": "Imports"
    },
    {
      "package": "rstan",
      "version": ">= 2.30.0",
      "role": "Imports"
    },
    {
      "package": "rstantools",
      "version": ">= 2.1.1",
      "role": "Imports"
    },
    {
      "package": "lubridate",
      "version": ">= 1.9.0",
      "role": "Imports"
    },
    {
      "package": "stars",
      "version": ">= 0.6-1",
      "role": "Imports"
    },
    {
      "package": "raster",
      "version": ">= 3.6-1",
      "role": "Imports"
    },
    {
      "package": "glmmrBase",
      "version": ">= 1.3.0",
      "role": "Imports"
    },
    {
      "package": "spdep",
      "role": "Imports"
    },
    {
      "package": "fmesher",
      "role": "Imports"
    },
    {
      "package": "FNN",
      "role": "Imports"
    },
    {
      "package": "quadprog",
      "role": "Imports"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-24",
      "n": 1
    },
    {
      "week": "2025-28",
      "n": 1
    },
    {
      "week": "2025-37",
      "n": 1
    },
    {
      "week": "2026-04",
      "n": 1
    },
    {
      "week": "2026-06",
      "n": 1
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [
    {
      "name": "0.8.0",
      "date": "2025-06-10"
    },
    {
      "name": "0.8.3",
      "date": "2025-07-08"
    },
    {
      "name": "0.9.1",
      "date": "2025-09-11"
    },
    {
      "name": "0.10.1",
      "date": "2026-01-20"
    },
    {
      "name": "0.10.2",
      "date": "2026-02-02"
    },
    {
      "name": "1.0.2",
      "date": "2026-04-30"
    }
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "samueliwatson",
      "count": 16,
      "uuid": 69966855
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 286,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rts2"
  },
  "_searchresults": 0,
  "_topics": [
    "cpp"
  ],
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/rts2.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.3",
      "date": "2022-03-21"
    },
    {
      "version": "0.4",
      "date": "2022-10-27"
    },
    {
      "version": "0.5",
      "date": "2023-04-18"
    },
    {
      "version": "0.6.1",
      "date": "2024-01-25"
    },
    {
      "version": "0.7.1",
      "date": "2024-03-01"
    },
    {
      "version": "0.7.2",
      "date": "2024-03-08"
    },
    {
      "version": "0.7.4",
      "date": "2024-04-04"
    },
    {
      "version": "0.7.5",
      "date": "2024-06-24"
    },
    {
      "version": "0.7.6",
      "date": "2024-09-06"
    },
    {
      "version": "0.7.7",
      "date": "2024-12-09"
    },
    {
      "version": "0.8.0",
      "date": "2025-06-10"
    },
    {
      "version": "0.8.3",
      "date": "2025-07-08"
    },
    {
      "version": "0.9.1",
      "date": "2025-09-11"
    },
    {
      "version": "0.10.1",
      "date": "2026-01-20"
    },
    {
      "version": "0.10.2",
      "date": "2026-02-02"
    },
    {
      "version": "1.0.2",
      "date": "2026-04-30"
    }
  ],
  "_exports": [
    "covariance.parameters",
    "create_points",
    "fixed.effects",
    "grid",
    "progress_bar",
    "random.effects"
  ],
  "_datasets": [
    {
      "name": "birmingham_crime",
      "title": "Birmingham crime data",
      "object": "birmingham_crime",
      "class": [
        "sf",
        "data.frame"
      ],
      "fields": [
        "MSOA21CD",
        "MSOA21NM",
        "BNG_E",
        "BNG_N",
        "LONG",
        "LAT",
        "GlobalID",
        "geometry",
        "t1",
        "t2",
        "t3",
        "t4",
        "t5",
        "t6",
        "t7",
        "t8",
        "t9",
        "t10",
        "t11",
        "t12",
        "pop"
      ],
      "rows": 132,
      "table": false,
      "tojson": true
    },
    {
      "name": "boundary",
      "title": "Boundary polygon for Birmingham, UK",
      "object": "boundary",
      "class": [
        "sf",
        "data.frame"
      ],
      "fields": [
        "weight",
        "geometry"
      ],
      "rows": 1,
      "table": false,
      "tojson": true
    },
    {
      "name": "example_points",
      "title": "Simulated point data for running single-period examples",
      "object": "example_points",
      "class": [
        "data.frame"
      ],
      "fields": [
        "X",
        "Y",
        "t"
      ],
      "rows": 261,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "rts2-package",
      "title": "Real-Time Disease Surveillance",
      "topics": [
        "rts2-package",
        "rts2"
      ]
    },
    {
      "page": "birmingham_crime",
      "title": "Birmingham crime data",
      "topics": [
        "birmingham_crime"
      ]
    },
    {
      "page": "boundary",
      "title": "Boundary polygon for Birmingham, UK",
      "topics": [
        "boundary"
      ]
    },
    {
      "page": "coef.rtsFit",
      "title": "Extracts fixed effect coefficients from a rtsFit object",
      "topics": [
        "coef.rtsFit"
      ]
    },
    {
      "page": "confint.rtsFit",
      "title": "Fixed effect confidence intervals for a 'rtsFit' object",
      "topics": [
        "confint.rtsFit"
      ]
    },
    {
      "page": "covariance.parameters",
      "title": "Extracts the estimates of the covariance parameters",
      "topics": [
        "covariance.parameters"
      ]
    },
    {
      "page": "create_points",
      "title": "Create sf object from point location data",
      "topics": [
        "create_points"
      ]
    },
    {
      "page": "disaggregate_covariate",
      "title": "Disaggregate regional means to fine grid, preserving aggregate means",
      "topics": [
        "disaggregate_covariate"
      ]
    },
    {
      "page": "disaggregate_positive",
      "title": "Disaggregation function for strictly positive covariates",
      "topics": [
        "disaggregate_positive"
      ]
    },
    {
      "page": "example_points",
      "title": "Simulated point data for running single-period examples",
      "topics": [
        "example_points"
      ]
    },
    {
      "page": "family.grid",
      "title": "Extracts the family from a 'grid' object.",
      "topics": [
        "family.grid"
      ]
    },
    {
      "page": "family.rtsFit",
      "title": "Extracts the family from a 'rtsFit' object.",
      "topics": [
        "family.rtsFit"
      ]
    },
    {
      "page": "fitted.rtsFit",
      "title": "Fitted values from a 'rtsFit' object",
      "topics": [
        "fitted.rtsFit"
      ]
    },
    {
      "page": "fixed.effects",
      "title": "Extracts the fixed effect estimates",
      "topics": [
        "fixed.effects"
      ]
    },
    {
      "page": "flat_disaggregate",
      "title": "Simple flat disaggregation",
      "topics": [
        "flat_disaggregate"
      ]
    },
    {
      "page": "formula.grid",
      "title": "Extracts the formula from a 'grid' object.",
      "topics": [
        "formula.grid"
      ]
    },
    {
      "page": "formula.rtsFit",
      "title": "Extracts the formula from a 'rtsFit' object.",
      "topics": [
        "formula.rtsFit"
      ]
    },
    {
      "page": "grid",
      "title": "An rts grid object",
      "topics": [
        "grid"
      ]
    },
    {
      "page": "logLik.rtsFit",
      "title": "Extracts the log-likelihood from an rtsFit object",
      "topics": [
        "logLik.rtsFit"
      ]
    },
    {
      "page": "predict.grid",
      "title": "Extract predictions from a 'grid' object",
      "topics": [
        "predict.grid"
      ]
    },
    {
      "page": "predict.rtsFit",
      "title": "Predict from a 'rtsFit' object",
      "topics": [
        "predict.rtsFit"
      ]
    },
    {
      "page": "print.rtsFit",
      "title": "Prints an rtsFit fit output",
      "topics": [
        "print.rtsFit"
      ]
    },
    {
      "page": "print.rtsFitSummary",
      "title": "Prints an rtsFitSummary fit output",
      "topics": [
        "print.rtsFitSummary"
      ]
    },
    {
      "page": "progress_bar",
      "title": "Generates a progress bar",
      "topics": [
        "progress_bar"
      ]
    },
    {
      "page": "random.effects",
      "title": "Extracts the random effect estimates",
      "topics": [
        "random.effects"
      ]
    },
    {
      "page": "residuals.grid",
      "title": "Residuals method for a 'grid' object",
      "topics": [
        "residuals.grid"
      ]
    },
    {
      "page": "residuals.rtsFit",
      "title": "Residuals method for a 'rtsFit' object",
      "topics": [
        "residuals.rtsFit"
      ]
    },
    {
      "page": "summary.grid",
      "title": "Summarizes a 'grid' object",
      "topics": [
        "summary.grid"
      ]
    },
    {
      "page": "summary.rtsFit",
      "title": "Summary method for class \"rtsFit\"",
      "topics": [
        "summary.rtsFit"
      ]
    },
    {
      "page": "vcov.grid",
      "title": "Calculate Variance-Covariance matrix for a maximum likelihood object stored in 'grid'",
      "topics": [
        "vcov.grid"
      ]
    },
    {
      "page": "vcov.rtsFit",
      "title": "Extract the Variance-Covariance matrix for a 'rtsFit' object",
      "topics": [
        "vcov.rtsFit"
      ]
    }
  ],
  "_readme": "https://github.com/cran/rts2/raw/HEAD/README.md",
  "_rundeps": [
    "abind",
    "backports",
    "BH",
    "boot",
    "callr",
    "checkmate",
    "class",
    "classInt",
    "cli",
    "cpp11",
    "DBI",
    "deldir",
    "desc",
    "distributional",
    "dplyr",
    "e1071",
    "farver",
    "fmesher",
    "FNN",
    "generics",
    "ggplot2",
    "glmmrBase",
    "glue",
    "gridExtra",
    "gtable",
    "inline",
    "isoband",
    "KernSmooth",
    "labeling",
    "lattice",
    "lifecycle",
    "loo",
    "lubridate",
    "magrittr",
    "MASS",
    "Matrix",
    "matrixStats",
    "numDeriv",
    "pillar",
    "pkgbuild",
    "pkgconfig",
    "posterior",
    "processx",
    "proxy",
    "ps",
    "quadprog",
    "QuickJSR",
    "R6",
    "raster",
    "RColorBrewer",
    "Rcpp",
    "RcppEigen",
    "RcppParallel",
    "rlang",
    "rstan",
    "rstantools",
    "s2",
    "S7",
    "scales",
    "sf",
    "sp",
    "spData",
    "spdep",
    "splancs",
    "StanHeaders",
    "stars",
    "tensorA",
    "terra",
    "tibble",
    "tidyselect",
    "timechange",
    "units",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "wk"
  ],
  "_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": 2.4771212547196626,
  "_indexed": true,
  "_nocasepkg": "rts2",
  "_universes": [
    "cran",
    "samueliwatson"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.2",
      "date": "2026-05-16T04:57:39.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "71f560d224226a8f315f535ec177bb47b9b00840",
      "fileid": "50951a6c6ec5831632c16e92679c30ebf2f27db77e0f7c2fd8d7acf0d5069dc3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25911497873"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.0.2",
      "date": "2026-05-16T04:57:41.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "71f560d224226a8f315f535ec177bb47b9b00840",
      "fileid": "220bf966a8582d8ba6f0c8575d003ef4c8e1e53d6a89d62435519a9684907f27",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25911497873"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.2",
      "date": "2026-05-15T10:01:29.000Z",
      "distro": "noble",
      "arch": "aarch64",
      "commit": "71f560d224226a8f315f535ec177bb47b9b00840",
      "fileid": "22ba722c041f7a3c4873596a30e60eb628799904628cf23261b4ae54f95dbc46",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25911497873"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.0.2",
      "date": "2026-05-15T10:01:44.000Z",
      "distro": "noble",
      "arch": "x86_64",
      "commit": "71f560d224226a8f315f535ec177bb47b9b00840",
      "fileid": "64a91a25361c22f2e0573c619a9772238a993c83f25d967c9f03a91ef216cac8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/25911497873"
    }
  ]
}