{
  "_id": "6acf61d0e2d863f662951725",
  "Package": "eppasm",
  "Title": "Age-structured EPP Model for HIV Epidemic Estimates",
  "Version": "0.8.6",
  "Authors@R": "person(\"Jeff\", \"Eaton\", email = \"jeffrey.eaton@imperial.ac.uk\", role = c(\"aut\", \"cre\"))",
  "Description": "Age-structured EPP Model for HIV Epidemic Estimates.",
  "Remotes": [
    "jeffeaton/anclik",
    "jeffeaton/epp"
  ],
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "VignetteBuilder": "knitr",
  "URL": "https://github.com/mrc-ide/eppasm,\nhttps://mrc-ide.github.io/eppasm/",
  "BugReports": "https://github.com/mrc-ide/eppasm/issues",
  "RoxygenNote": "7.2.3",
  "Config/pak/sysreqs": "libicu-dev libxml2-dev",
  "Repository": "https://mrc-ide.r-universe.dev",
  "Date/Publication": "2025-12-03 11:24:15 UTC",
  "RemoteUrl": "https://github.com/mrc-ide/eppasm",
  "RemoteRef": "master",
  "RemoteSha": "e25b33fab24238f0937252018f58afcb1de43b71",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-14 10:58:08 UTC",
    "User": "root"
  },
  "Author": "Jeff Eaton [aut, cre]",
  "Maintainer": "Jeff Eaton <jeffrey.eaton@imperial.ac.uk>",
  "_user": "mrc-ide",
  "_type": "src",
  "_file": "eppasm_0.8.6.tar.gz",
  "_fileid": "https://r2.ropensci.org/62a8f301dcf48c5a57a8954fa548221b1221bace2d002a8186b22891901b1fdf",
  "_filesize": 15671746,
  "_sha256": "62a8f301dcf48c5a57a8954fa548221b1221bace2d002a8186b22891901b1fdf",
  "_expires": "2027-01-22T11:04:45.000Z",
  "_created": "2026-10-14T10:58:08.000Z",
  "_published": "2026-10-14T11:04:48.257Z",
  "_buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 115816253917,
      "time": 175,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11888295079"
    },
    {
      "job": 115816254002,
      "time": 167,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11887124441"
    },
    {
      "job": 115816253952,
      "time": 142,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11888275126"
    },
    {
      "job": 115816254512,
      "time": 185,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11887034715"
    },
    {
      "job": 115816253943,
      "time": 158,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11888130323"
    },
    {
      "job": 115816253880,
      "time": 301,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11887817166"
    },
    {
      "job": 115816254058,
      "time": 112,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11888055539"
    },
    {
      "job": 115816254018,
      "time": 341,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11887404106"
    },
    {
      "job": 115814928554,
      "time": 208,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11887587536"
    },
    {
      "job": 115816254043,
      "time": 138,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11887577942"
    },
    {
      "job": 115816253936,
      "time": 234,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11887668007"
    },
    {
      "job": 115816254317,
      "time": 170,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11887702600"
    },
    {
      "job": 115816253901,
      "time": 156,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11888110435"
    },
    {
      "job": 115816253966,
      "time": 236,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11887628046"
    },
    {
      "job": 115816254006,
      "time": 140,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11888035693"
    }
  ],
  "_upstream": "https://github.com/mrc-ide/eppasm",
  "_commit": {
    "id": "e25b33fab24238f0937252018f58afcb1de43b71",
    "author": "Rob Ashton <robertashton94@gmail.com>",
    "committer": "Rob Ashton <robertashton94@gmail.com>",
    "message": "Update pkgdown to latest setup from usethis\n",
    "time": 1764761055
  },
  "_maintainer": {
    "name": "Jeff Eaton",
    "email": "jeffrey.eaton@imperial.ac.uk",
    "login": "jeffeaton",
    "description": "",
    "uuid": 7427899
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.1.0",
      "role": "Depends"
    },
    {
      "package": "BH",
      "role": "LinkingTo"
    },
    {
      "package": "abind",
      "version": ">= 1.4",
      "role": "Imports"
    },
    {
      "package": "anclik",
      "role": "Imports"
    },
    {
      "package": "binom",
      "role": "Imports"
    },
    {
      "package": "epp",
      "version": ">= 0.4.1",
      "role": "Imports"
    },
    {
      "package": "fastmatch",
      "version": ">= 1.1",
      "role": "Imports"
    },
    {
      "package": "mvtnorm",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "readxl",
      "role": "Imports"
    },
    {
      "package": "reshape2",
      "role": "Imports"
    },
    {
      "package": "vroom",
      "role": "Imports"
    },
    {
      "package": "xml2",
      "role": "Imports"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    }
  ],
  "_owner": "mrc-ide",
  "_selfowned": true,
  "_usedby": 4,
  "_updates": [
    {
      "week": "2025-44",
      "n": 1
    },
    {
      "week": "2025-49",
      "n": 2
    }
  ],
  "_tags": [],
  "_stars": 6,
  "_contributors": [
    {
      "user": "jeffeaton",
      "count": 369,
      "uuid": 7427899
    },
    {
      "user": "r-ash",
      "count": 18,
      "uuid": 39248272
    },
    {
      "user": "mwalte10",
      "count": 2,
      "uuid": 24323420
    },
    {
      "user": "m-kusumgar",
      "count": 1,
      "uuid": 98405247
    },
    {
      "user": "rlglaubius",
      "count": 1,
      "uuid": 23197978
    }
  ],
  "_userbio": {
    "uuid": 25453642,
    "type": "organization",
    "name": "MRC Centre for Global Infectious Disease Analysis",
    "followers": 164,
    "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/eppasm"
  },
  "_devurl": "https://github.com/mrc-ide/eppasm",
  "_pkgdown": "https://mrc-ide.github.io/eppasm/",
  "_searchresults": 23,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/eppasm.html",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_cranurl": false,
  "_exports": [
    "agepregartcov",
    "agepregprev",
    "ageprev",
    "ageprev.specres",
    "aggr_specres",
    "aidsdeaths.specres",
    "ancsite_pred_df",
    "artcov15plus",
    "artcov15to49",
    "calc_incid15to49",
    "calc_pregprev",
    "calc_prev15to49",
    "create_spectrum_fixpar",
    "fitmod",
    "fnCreateParam",
    "fnPregPrev",
    "hivpop_singleage",
    "incid",
    "incid15to49_eppinput_specres",
    "ll",
    "ll_ancrtcens",
    "ll_ancsite",
    "ll_hhsage",
    "ll_hhsage_binom",
    "lprior",
    "mod_dimnames",
    "prepare_directincid",
    "prepare_likdat",
    "prepare_rhybrid",
    "prepare_spec_fit",
    "prev",
    "read_country",
    "read_csavr_data",
    "read_demog_param",
    "read_dp",
    "read_epp_perc_urban",
    "read_epp_t0",
    "read_hivproj_output",
    "read_hivproj_param",
    "read_incid_input",
    "read_iso3",
    "read_pjn",
    "read_pop1",
    "read_region",
    "read_specdp_demog_param",
    "read_subp_file",
    "simmod",
    "spec_add_dimnames",
    "tidy_output"
  ],
  "_help": [
    {
      "page": "agemx.spec",
      "title": "Age-specific mortality",
      "topics": [
        "agemx.spec"
      ]
    },
    {
      "page": "agepregartcov",
      "title": "Age-specific ART coverage among pregnant women",
      "topics": [
        "agepregartcov"
      ]
    },
    {
      "page": "agepregprev",
      "title": "Age-specific prevalence among pregnant women",
      "topics": [
        "agepregprev"
      ]
    },
    {
      "page": "ageprev",
      "title": "Prevalence by arbitrary age groups",
      "topics": [
        "ageprev"
      ]
    },
    {
      "page": "ancsite_pred_df",
      "title": "Prepare design matrix indices for ANC prevalence predictions",
      "topics": [
        "ancsite_pred_df"
      ]
    },
    {
      "page": "calc_infections_eppspectrum",
      "title": "Annualized number of new infections",
      "topics": [
        "calc_infections_eppspectrum"
      ]
    },
    {
      "page": "create_spectrum_fixpar",
      "title": "Create simulation inputs fixed parameters",
      "topics": [
        "create_spectrum_fixpar"
      ]
    },
    {
      "page": "get_proj_years",
      "title": "Get vector of years spanned by projections",
      "topics": [
        "get_proj_years"
      ]
    },
    {
      "page": "hivpop_singleage",
      "title": "Convert aggregate HIV population to single year",
      "topics": [
        "hivpop_singleage"
      ]
    },
    {
      "page": "imis",
      "title": "Incremental Mixture Importance Sampling (IMIS)",
      "topics": [
        "imis"
      ]
    },
    {
      "page": "incid",
      "title": "Incidence rate among adults age 15-49 years",
      "topics": [
        "incid"
      ]
    },
    {
      "page": "incid15to49_eppinput_specres",
      "title": "Incidence rate age 15-49 using previous-year susceptible population",
      "topics": [
        "incid15to49_eppinput_specres"
      ]
    },
    {
      "page": "ll_ancsite_conditional",
      "title": "Pointwise likelihood for site-level ANC observations given site-level effects",
      "topics": [
        "ll_ancsite_conditional"
      ]
    },
    {
      "page": "ll_hhsage",
      "title": "Log likelihood for age-specific household survey prevalence",
      "topics": [
        "ll_hhsage"
      ]
    },
    {
      "page": "ll_hhsage_binom",
      "title": "Log likelihood for age-specific household survey prevalence using binomial approximation",
      "topics": [
        "ll_hhsage_binom"
      ]
    },
    {
      "page": "ll_hhsartcov",
      "title": "Log likelihood for age-specific household survey prevalence",
      "topics": [
        "ll_hhsartcov"
      ]
    },
    {
      "page": "ll_hhsincid",
      "title": "Log-likelhood for direct incidence estimate from household survey",
      "topics": [
        "ll_hhsincid"
      ]
    },
    {
      "page": "melt_ancsite_data",
      "title": "Melt ANC-SS and site-level ANC-RT to long dataset",
      "topics": [
        "melt_ancsite_data"
      ]
    },
    {
      "page": "mod_dimnames",
      "title": "Add dimnames to spec model output",
      "topics": [
        "mod_dimnames"
      ]
    },
    {
      "page": "natagemx.spec",
      "title": "Non-HIV age-specific mortality",
      "topics": [
        "natagemx.spec"
      ]
    },
    {
      "page": "prepare_ancsite_likdat",
      "title": "Prepare site-level ANC prevalence data for EPP random-effects likelihood",
      "topics": [
        "prepare_ancsite_likdat"
      ]
    },
    {
      "page": "prepare_directincid",
      "title": "Prepare direct incidence input EPP simulation",
      "topics": [
        "prepare_directincid"
      ]
    },
    {
      "page": "prepare_hhsageprev_likdat",
      "title": "Prepare age-specific HH survey prevalence likelihood data",
      "topics": [
        "prepare_hhsageprev_likdat"
      ]
    },
    {
      "page": "prepare_hhsartcov_likdat",
      "title": "## Household survey ART coverage likelihood",
      "topics": [
        "prepare_hhsartcov_likdat"
      ]
    },
    {
      "page": "prepare_hhsincid_likdat",
      "title": "Prepare household survey incidence likelihood data",
      "topics": [
        "prepare_hhsincid_likdat"
      ]
    },
    {
      "page": "prepare_rhybrid",
      "title": "Setup the r-hybrid model",
      "topics": [
        "prepare_rhybrid"
      ]
    },
    {
      "page": "prepare_spec_fit",
      "title": "Prepare fit by EPP regions",
      "topics": [
        "prepare_spec_fit"
      ]
    },
    {
      "page": "read_csavr_data",
      "title": "Read CSAVR input data",
      "topics": [
        "read_csavr_data"
      ]
    },
    {
      "page": "read_dp",
      "title": "Read Spectrum internal files file from PJNZ",
      "topics": [
        "read_dp"
      ]
    },
    {
      "page": "read_incid_input",
      "title": "Read annual incidence input",
      "topics": [
        "read_incid_input"
      ]
    },
    {
      "page": "read_pop1",
      "title": "Read Spectrum _pop1.xlsx export file",
      "topics": [
        "read_pop1"
      ]
    },
    {
      "page": "sample_ancsite_pred",
      "title": "Sample posterior predictions for site-level ANC observations",
      "topics": [
        "sample_ancsite_pred"
      ]
    },
    {
      "page": "sample_b_site",
      "title": "Sample from posterior ditribution for ANC site level random effects",
      "topics": [
        "sample_b_site"
      ]
    },
    {
      "page": "sample_invgamma_post",
      "title": "Sample from conditional posterior distribution for variance parameter",
      "topics": [
        "sample_invgamma_post"
      ]
    },
    {
      "page": "simmod",
      "title": "Simulate model",
      "topics": [
        "simmod"
      ]
    },
    {
      "page": "spec_add_dimnames",
      "title": "Add dimnames to EPP-ASM model output",
      "topics": [
        "spec_add_dimnames"
      ]
    }
  ],
  "_readme": "https://github.com/mrc-ide/eppasm/raw/master/README.md",
  "_rundeps": [
    "abind",
    "anclik",
    "BH",
    "binom",
    "bit",
    "bit64",
    "cellranger",
    "cli",
    "cpp11",
    "crayon",
    "epp",
    "fastmatch",
    "glue",
    "hms",
    "lifecycle",
    "magrittr",
    "mvtnorm",
    "pillar",
    "pkgconfig",
    "plyr",
    "prettyunits",
    "progress",
    "R6",
    "Rcpp",
    "readxl",
    "rematch",
    "reshape2",
    "rlang",
    "stringi",
    "stringr",
    "tibble",
    "tidyselect",
    "tzdb",
    "utf8",
    "vctrs",
    "vroom",
    "withr",
    "xml2"
  ],
  "_score": 4.821120323776824,
  "_indexed": true,
  "_nocasepkg": "eppasm",
  "_universes": [
    "mrc-ide",
    "jeffeaton"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.8.6",
      "date": "2026-10-14T11:00:50.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/3d7f0ed4577d35e96cc68944bae5e5d42ec0765ee555cec39017279cf1b765a8",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.8.6",
      "date": "2026-10-14T11:00:32.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/15fe2b7f7e2e63813c4ab5377eadb02bfe402cbc7df3be7b50c107b83da9011d",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.8.6",
      "date": "2026-10-14T11:00:18.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/2632df2bf17a1dd5c02e3ad4198df6d0e6120a4e9a80f717f8b699d8affe3f3e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "0.8.6",
      "date": "2026-10-14T11:00:53.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/1203aec4cb456c81cc92dd9af48a5d8e0eea4bb8277fce46b1ac4cc11c345396",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.8.6",
      "date": "2026-10-14T11:00:29.000Z",
      "arch": "aarch64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/6cf280d4f97ca9d6c62a927dcbe020821dee92311e6ad97cef8952e0319d49af",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.8.6",
      "date": "2026-10-14T11:02:06.000Z",
      "arch": "x86_64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/36f9f3c257916ec8fbbb4e24a119ef39fec87b3a228926d1ef13950dc74819dd",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.8.6",
      "date": "2026-10-14T10:59:57.000Z",
      "arch": "aarch64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/a2909908eb814b1e2a213cfa0ddf0f383f33e7b865d6fb40e7306554e30ef349",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "0.8.6",
      "date": "2026-10-14T11:02:52.000Z",
      "arch": "x86_64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/ef6286ad161bc0000ebaab6f62137328602528bdd8aae21cc84776a3d340834f",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.8.6",
      "date": "2026-10-14T11:00:43.000Z",
      "arch": "emscripten",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/c1d8fb575d65c671a4a5ce51674b9ec8b2257c047966c9ba48cdcb31a11a2907",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.8.6",
      "date": "2026-10-14T11:01:30.000Z",
      "arch": "aarch64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/3f454cd711b127797789bedb62f5847ed82ba0eb1b8e9384fee770857fe3b04f",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.8.6",
      "date": "2026-10-14T10:59:45.000Z",
      "arch": "x86_64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/1c465d6a511d4aa9b1dc2ede2aed132e2bb79a303ea7c23bf438fc108dcc4c7b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.8.6",
      "date": "2026-10-14T10:59:49.000Z",
      "arch": "x86_64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/4ed4cb12ebb2710d41bb7a9371bb368839d49fcd34cccf98e3613189b5665b1e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.8.6",
      "date": "2026-10-14T11:01:38.000Z",
      "arch": "aarch64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/babccd921c7bfcf1feab86d49546f0759d3c135bc682a7dc880669edb7e27e3b",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "0.8.6",
      "date": "2026-10-14T10:59:45.000Z",
      "arch": "x86_64",
      "commit": "e25b33fab24238f0937252018f58afcb1de43b71",
      "fileid": "https://r2.ropensci.org/432f4fbc61bd091d1372573ca113b9fd7d04958005e72eb11f20c5d189aa8c35",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mrc-ide/actions/runs/38552843535"
    }
  ]
}