{
  "_id": "6a490503b5e98c4082a0681c",
  "Package": "EpiLPS",
  "Type": "Package",
  "Title": "A Fast and Flexible Bayesian Tool for Estimating Epidemiological\nParameters",
  "Version": "1.4.0",
  "Authors@R": "c(person(\"Oswaldo\",\"Gressani\", \nemail=\"oswaldo_gressani@hotmail.fr\", role=c(\"aut\",\"cre\"),\ncomment=c(ORCID =\"0000-0003-4152-6159\")),\nperson(\"Bryan\", \"Sumalinab\", role = \"ctb\", comment=c(ORCID =\"0000-0001-8264-5336\"))\n)",
  "Maintainer": "Oswaldo Gressani <oswaldo_gressani@hotmail.fr>",
  "BugReports": "https://github.com/oswaldogressani/EpiLPS/issues",
  "Description": "Estimation of epidemiological parameters with\nLaplacian-P-splines following the methodology of Gressani et\nal. (2022) <doi:10.1371/journal.pcbi.1010618>.",
  "URL": "<https://epilps.com/>",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libicu-dev",
  "Repository": "https://oswaldogressani.r-universe.dev",
  "Date/Publication": "2025-09-01 14:04:15 UTC",
  "RemoteUrl": "https://github.com/oswaldogressani/epilps",
  "RemoteRef": "HEAD",
  "RemoteSha": "cece691109c64725f5ab8d279d27c960141f1e9b",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-07-04 13:00:10 UTC",
    "User": "root"
  },
  "Author": "Oswaldo Gressani [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4152-6159>),\nBryan Sumalinab [ctb] (ORCID: <https://orcid.org/0000-0001-8264-5336>)",
  "_user": "oswaldogressani",
  "_type": "src",
  "_file": "EpiLPS_1.4.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/293d15ea82ecdb18f3f2faf10123ac6409f74b3f98690ad24aa1c77906a3a2a4",
  "_filesize": 297055,
  "_sha256": "293d15ea82ecdb18f3f2faf10123ac6409f74b3f98690ad24aa1c77906a3a2a4",
  "_expires": "2026-10-12T13:05:05.000Z",
  "_created": "2026-07-04T13:00:10.000Z",
  "_published": "2026-07-04T13:05:07.152Z",
  "_jobs": [
    {
      "job": 85134309191,
      "time": 191,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8081950034"
    },
    {
      "job": 85134309195,
      "time": 195,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8081950131"
    },
    {
      "job": 85134309214,
      "time": 196,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8081950512"
    },
    {
      "job": 85134309194,
      "time": 182,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8081948707"
    },
    {
      "job": 85134309228,
      "time": 100,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8081939330"
    },
    {
      "job": 85134309254,
      "time": 203,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8081950904"
    },
    {
      "job": 85134309251,
      "time": 119,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8081941348"
    },
    {
      "job": 85134309211,
      "time": 226,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8081953574"
    },
    {
      "job": 85134040914,
      "time": 244,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8081926728"
    },
    {
      "job": 85134309190,
      "time": 192,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "8081949875"
    },
    {
      "job": 85134309200,
      "time": 153,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "8081945436"
    },
    {
      "job": 85134309197,
      "time": 161,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "8081946266"
    },
    {
      "job": 85134309201,
      "time": 177,
      "config": "windows-release",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "8081947985"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463",
  "_status": "success",
  "_upstream": "https://github.com/oswaldogressani/epilps",
  "_commit": {
    "id": "cece691109c64725f5ab8d279d27c960141f1e9b",
    "author": "oswaldogressani <oswaldo_gressani@hotmail.fr>",
    "committer": "oswaldogressani <oswaldo_gressani@hotmail.fr>",
    "message": "Removal of SI routine, moved to EpiDelays package\n",
    "time": 1756735455
  },
  "_maintainer": {
    "name": "Oswaldo Gressani",
    "email": "oswaldo_gressani@hotmail.fr",
    "login": "oswaldogressani",
    "twitter": "@OswaldoGressani",
    "description": "Postdoctoral researcher at Hasselt University with a focus on mathematical modeling of infectious diseases and approximate Bayesian inference.",
    "uuid": 68177358,
    "orcid": "0000-0003-4152-6159"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "RcppArmadillo",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "Rcpp",
      "version": ">= 1.0.7",
      "role": "Imports"
    },
    {
      "package": "coda",
      "version": ">= 0.19-4",
      "role": "Imports"
    },
    {
      "package": "EpiEstim",
      "version": ">= 2.2-4",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "version": ">= 3.3.5",
      "role": "Imports"
    },
    {
      "package": "gridExtra",
      "version": ">= 2.3",
      "role": "Imports"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    }
  ],
  "_owner": "oswaldogressani",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-36",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 21,
  "_contributors": [
    {
      "user": "oswaldogressani",
      "count": 51,
      "uuid": 68177358
    }
  ],
  "_userbio": {
    "uuid": 68177358,
    "type": "user",
    "name": "Oswaldo Gressani",
    "followers": 27,
    "description": "Postdoctoral researcher at Hasselt University with a focus on mathematical modeling of infectious diseases and approximate Bayesian inference."
  },
  "_downloads": {
    "count": 440,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/EpiLPS"
  },
  "_devurl": "https://github.com/oswaldogressani/epilps",
  "_searchresults": 26,
  "_topics": [
    "openblas",
    "cpp",
    "openmp"
  ],
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/EpiLPS.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/oswaldogressani/epilps",
  "_realowner": "oswaldogressani",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0.1",
      "date": "2021-12-21"
    },
    {
      "version": "1.0.2",
      "date": "2022-01-03"
    },
    {
      "version": "1.0.5",
      "date": "2022-05-06"
    },
    {
      "version": "1.0.6",
      "date": "2022-08-08"
    },
    {
      "version": "1.0.7",
      "date": "2023-01-18"
    },
    {
      "version": "1.1.0",
      "date": "2023-04-05"
    },
    {
      "version": "1.2.0",
      "date": "2023-08-30"
    },
    {
      "version": "1.3.0",
      "date": "2024-03-08"
    }
  ],
  "_exports": [
    "epicurve",
    "episim",
    "estimIncub",
    "estimR",
    "estimRmcmc",
    "histosmooth",
    "Idist",
    "incubsim",
    "nowcasting",
    "nowcastingR",
    "perfRestim",
    "Rmodelpriors"
  ],
  "_datasets": [
    {
      "name": "cov19incidence2022",
      "title": "Incidence data for Belgium in 2022",
      "object": "cov19incidence2022",
      "class": [
        "data.frame"
      ],
      "fields": [
        "t",
        "d",
        "Date",
        "Rep.date",
        "Cases",
        "Reported"
      ],
      "rows": 540,
      "table": true,
      "tojson": true
    },
    {
      "name": "cov19mort2021",
      "title": "Mortality data for Belgium in 2021",
      "object": "cov19mort2021",
      "class": [
        "data.frame"
      ],
      "fields": [
        "t",
        "d",
        "Date",
        "Rep.date",
        "Cases",
        "Reported"
      ],
      "rows": 546,
      "table": true,
      "tojson": true
    },
    {
      "name": "eruptions",
      "title": "Eruption times in Yellowstone National Park",
      "object": "eruptions",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "influenza2009",
      "title": "Data on the 2009 pandemic influenza in Pennsylvania",
      "object": "influenza2009",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "influenza2009serial",
      "title": "Serial interval data for the 2009 outbreak of pandemic Influenza A (H1N1)",
      "object": "influenza2009serial",
      "class": [
        "data.frame"
      ],
      "fields": [
        "SL",
        "SR"
      ],
      "rows": 16,
      "table": true,
      "tojson": true
    },
    {
      "name": "sars2003",
      "title": "Daily incidence of the 2003 SARS epidemic in Hong Kong",
      "object": "sars2003",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "zika2015",
      "title": "Data on the 2015 Zika virus disease in Colombia",
      "object": "zika2015",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "cov19incidence2022",
      "title": "Incidence data for Belgium in 2022",
      "topics": [
        "cov19incidence2022"
      ]
    },
    {
      "page": "cov19mort2021",
      "title": "Mortality data for Belgium in 2021",
      "topics": [
        "cov19mort2021"
      ]
    },
    {
      "page": "epicurve",
      "title": "Plot the epidemic curve",
      "topics": [
        "epicurve"
      ]
    },
    {
      "page": "episim",
      "title": "Simulation of an incidence time series",
      "topics": [
        "episim"
      ]
    },
    {
      "page": "eruptions",
      "title": "Eruption times in Yellowstone National Park",
      "topics": [
        "eruptions"
      ]
    },
    {
      "page": "estimIncub",
      "title": "Estimation of the incubation density based on coarse data",
      "topics": [
        "estimIncub"
      ]
    },
    {
      "page": "estimR",
      "title": "Estimation of the reproduction number with Laplacian-P-splines",
      "topics": [
        "estimR"
      ]
    },
    {
      "page": "estimRmcmc",
      "title": "Estimation of the reproduction number with Laplacian-P-splines via MCMC",
      "topics": [
        "estimRmcmc"
      ]
    },
    {
      "page": "histosmooth",
      "title": "Histogram smoothing with Laplacian-P-splines",
      "topics": [
        "histosmooth"
      ]
    },
    {
      "page": "Idist",
      "title": "Density function and discrete distribution for a disease interval",
      "topics": [
        "Idist"
      ]
    },
    {
      "page": "incubsim",
      "title": "Simulation of incubation times",
      "topics": [
        "incubsim"
      ]
    },
    {
      "page": "influenza2009",
      "title": "Data on the 2009 pandemic influenza in Pennsylvania",
      "topics": [
        "influenza2009"
      ]
    },
    {
      "page": "influenza2009serial",
      "title": "Serial interval data for the 2009 outbreak of pandemic Influenza A (H1N1)",
      "topics": [
        "influenza2009serial"
      ]
    },
    {
      "page": "nowcasting",
      "title": "Nowcasting and estimation of occurred but not yet reported events",
      "topics": [
        "nowcasting"
      ]
    },
    {
      "page": "nowcastingR",
      "title": "Nowcasting the reproduction number",
      "topics": [
        "nowcastingR"
      ]
    },
    {
      "page": "perfRestim",
      "title": "Routine to measure the performance of estimR and estimRmcmc",
      "topics": [
        "perfRestim"
      ]
    },
    {
      "page": "plot.Idist",
      "title": "Plot the interval distribution from an Idist object",
      "topics": [
        "plot.Idist"
      ]
    },
    {
      "page": "plot.incubestim",
      "title": "Plot the estimated incubation distribution",
      "topics": [
        "plot.incubestim"
      ]
    },
    {
      "page": "plot.nowcasted",
      "title": "Plot of nowcasted cases and delay distribution",
      "topics": [
        "plot.nowcasted"
      ]
    },
    {
      "page": "plot.Rt",
      "title": "Plot the estimated reproduction number",
      "topics": [
        "plot.Rt"
      ]
    },
    {
      "page": "plot.Rtnow",
      "title": "Plot the nowcasted reproduction number",
      "topics": [
        "plot.Rtnow"
      ]
    },
    {
      "page": "Rmodelpriors",
      "title": "Prior specification for model hyperparameters",
      "topics": [
        "Rmodelpriors"
      ]
    },
    {
      "page": "sars2003",
      "title": "Daily incidence of the 2003 SARS epidemic in Hong Kong",
      "topics": [
        "sars2003"
      ]
    },
    {
      "page": "summary.Rt",
      "title": "Summarize the estimated reproduction number",
      "topics": [
        "summary.Rt"
      ]
    },
    {
      "page": "zika2015",
      "title": "Data on the 2015 Zika virus disease in Colombia",
      "topics": [
        "zika2015"
      ]
    }
  ],
  "_readme": "https://github.com/oswaldogressani/epilps/raw/HEAD/README.md",
  "_rundeps": [
    "aweek",
    "cli",
    "coarseDataTools",
    "coda",
    "cpp11",
    "EpiEstim",
    "farver",
    "fitdistrplus",
    "ggplot2",
    "glue",
    "gridExtra",
    "gtable",
    "incidence",
    "isoband",
    "labeling",
    "lattice",
    "lifecycle",
    "magrittr",
    "MASS",
    "Matrix",
    "MatrixModels",
    "mcmc",
    "MCMCpack",
    "plyr",
    "quantreg",
    "R6",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "reshape2",
    "rlang",
    "S7",
    "scales",
    "SparseM",
    "stringi",
    "stringr",
    "survival",
    "vctrs",
    "viridisLite",
    "withr"
  ],
  "_sysdeps": [
    {
      "shlib": "liblapack",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    },
    {
      "shlib": "libgomp",
      "package": "libgomp1",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "openmp",
      "homepage": "http://gcc.gnu.org/",
      "description": "GCC OpenMP (GOMP) support library"
    }
  ],
  "_score": 4.4361626470407565,
  "_indexed": true,
  "_nocasepkg": "epilps",
  "_universes": [
    "oswaldogressani"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4.0",
      "date": "2026-07-04T13:03:26.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/4163048f5f5fb1db30c64651ebd49b956c8bb2ab04666a24fc64fecd3c8018bf",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.4.0",
      "date": "2026-07-04T13:03:16.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/86b91e001f4b469f359aef3550aa2e400507ba4392fc1576f0b1c991f49d1bf4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.4.0",
      "date": "2026-07-04T13:03:30.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/3142bf87daef0fac251f8808cbd9dcf13f757f73c3e1a987bab5ebcde485e97d",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.4.0",
      "date": "2026-07-04T13:03:05.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/4a3f40f32a176a4ddddc8fc3e2d495adfb33f751806a65641ee96f9ad8417f29",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4.0",
      "date": "2026-07-04T13:02:11.000Z",
      "arch": "aarch64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/db81b939cdd401ac5f41a667c85c9b494bc29625a530992e9b2461e4b87617fd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.4.0",
      "date": "2026-07-04T13:03:04.000Z",
      "arch": "x86_64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/ea70c374d888285523d330794753a90cc0d5ebc2d126744682de5e617226c1a6",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.4.0",
      "date": "2026-07-04T13:02:15.000Z",
      "arch": "aarch64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/1d3447abd9ee5b616b419524a25c1e75d371bc2db1edc143a7f58896d3e24775",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.4.0",
      "date": "2026-07-04T13:03:24.000Z",
      "arch": "x86_64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/cbe1b2da49cffa2461e01eb41883796686222a9d6106795bcac48a291023ea89",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.4.0",
      "date": "2026-07-04T13:03:38.000Z",
      "arch": "emscripten",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/fa4da73f7d1d2b5071d5ea87de71324505107ee206dc30c0ecd17b19512b449e",
      "status": "success",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.4.0",
      "date": "2026-07-04T13:02:03.000Z",
      "arch": "x86_64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/cc53457a2d6fc12dd539abaa18026087a72b373f75d7231c10343161a17a2c04",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.4.0",
      "date": "2026-07-04T13:02:03.000Z",
      "arch": "x86_64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/68840d6e3896cf52cac52038b3250de38cb2f9eaf71075fbccc93ae213936c52",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.4.0",
      "date": "2026-07-04T13:02:03.000Z",
      "arch": "x86_64",
      "commit": "cece691109c64725f5ab8d279d27c960141f1e9b",
      "fileid": "https://r2.ropensci.org/36ebbf0d056aad2cb82feb17ea8234b3e4b9eb8ec5165d30ac947e33ac28ce3e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/oswaldogressani/actions/runs/28706917463"
    }
  ]
}