{ "_id": "6a20750bcd65a98ecbd12fa4", "Package": "epiparameter", "Title": "Classes and Helper Functions for Working with Epidemiological\nParameters", "Version": "0.4.1.9000", "Authors@R": "c(\nperson(\"Joshua W.\", \"Lambert\", , \"joshua.lambert@lshtm.ac.uk\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-5218-3046\")),\nperson(\"Adam\", \"Kucharski\", , \"adam.kucharski@lshtm.ac.uk\", role = c(\"aut\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-8814-9421\")),\nperson(\"Carmen\", \"Tamayo Cuartero\", , \"carmen.tamayo-cuartero@lshtm.ac.uk\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-4184-2864\")),\nperson(\"Hugo\", \"Gruson\", , \"hugo.gruson@data.org\", role = c(\"ctb\", \"rev\"),\ncomment = c(ORCID = \"0000-0002-4094-1476\")),\nperson(\"Sebastian\", \"Funk\", , \"sebastian.funk@lshtm.ac.uk\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-2842-3406\")),\nperson(\"Pratik\", \"Gupte\", , \"pratik.gupte@lshtm.ac.uk\", role = \"rev\",\ncomment = c(ORCID = \"0000-0001-5294-7819\")),\nperson(\"James M.\", \"Azam\", , \"james.azam@lshtm.ac.uk\", role = \"rev\",\ncomment = c(ORCID = \"0000-0001-5782-7330\")),\nperson(\"Chris\", \"Hartgerink\", , \"chris@data.org\", role = \"rev\",\ncomment = c(ORCID = \"0000-0003-1050-6809\")),\nperson(\"Tim\", \"Taylor\", , \"tim.taylor@hiddenelephants.co.uk\", role = \"rev\",\ncomment = c(ORCID = \"0000-0002-8587-7113\")),\nperson(\"London School of Hygiene and Tropical Medicine, LSHTM\", role = \"cph\",\ncomment = c(ROR = \"00a0jsq62\"))\n)", "Description": "Classes and helper functions for loading, extracting,\nconverting, manipulating, plotting and aggregating\nepidemiological parameters for infectious diseases.\nEpidemiological parameters extracted from the literature are\nloaded from the 'epiparameterDB' R package.", "License": "MIT + file LICENSE", "URL": "https://github.com/epiverse-trace/epiparameter/,\nhttps://epiverse-trace.github.io/epiparameter/", "BugReports": "https://github.com/epiverse-trace/epiparameter/issues", "Remotes": [ "epiverse-trace/epiparameterDB" ], "VignetteBuilder": "knitr", "Config/Needs/check": "mrc-ide/epireview", "Config/Needs/website": "epiverse-trace/epiversetheme, mrc-ide/epireview", "Config/potools/style": "explicit", "Config/testthat/edition": "3", "Encoding": "UTF-8", "Language": "en-GB", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "libssl-dev", "Repository": "https://epiverse-trace.r-universe.dev", "Date/Publication": "2026-06-03 17:21:52 UTC", "RemoteUrl": "https://github.com/epiverse-trace/epiparameter", "RemoteRef": "HEAD", "RemoteSha": "291bfd2490cc4c59f002652d3100139c64499107", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-03 18:32:59 UTC", "User": "root" }, "Author": "Joshua W. Lambert [aut, cre, cph] (ORCID:\n),\nAdam Kucharski [aut, cph] (ORCID:\n),\nCarmen Tamayo Cuartero [aut] (ORCID:\n),\nHugo Gruson [ctb, rev] (ORCID: ),\nSebastian Funk [ctb] (ORCID: ),\nPratik Gupte [rev] (ORCID: ),\nJames M. Azam [rev] (ORCID: ),\nChris Hartgerink [rev] (ORCID: ),\nTim Taylor [rev] (ORCID: ),\nLondon School of Hygiene and Tropical Medicine, LSHTM [cph] (ROR:\n)", "Maintainer": "Joshua W. Lambert ", "MD5sum": "966c0a4af6bbabaf3fe56f0dc865daf5", "_user": "epiverse-trace", "_type": "src", "_file": "epiparameter_0.4.1.9000.tar.gz", "_fileid": "ba699167ba13bb26c1c0c9b5ec010cf84c9a4e6cddccd6acd42be15a2e7991c3", "_filesize": 721422, "_sha256": "ba699167ba13bb26c1c0c9b5ec010cf84c9a4e6cddccd6acd42be15a2e7991c3", "_created": "2026-06-03T18:32:59.000Z", "_published": "2026-06-03T18:40:11.791Z", "_distro": "noble", "_jobs": [ { "job": 79367677410, "time": 206, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7393532018" }, { "job": 79367677502, "time": 209, "config": "linux-release-x86_64", "r": "4.6.0", "check": "OK", "artifact": "7393533625" }, { "job": 79367677493, "time": 156, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "7393526385" }, { "job": 79367677687, "time": 206, "config": "macos-release-arm64", "r": "4.6.0", "check": "OK", "artifact": "7393596656" }, { "job": 79366970001, "time": 216, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7393455104" }, { "job": 79367677579, "time": 117, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7393500323" }, { "job": 79367677457, "time": 223, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7393538362" }, { "job": 79367677492, "time": 230, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7393542665" }, { "job": 79367677441, "time": 229, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7393540950" } ], "_buildurl": "https://github.com/r-universe/epiverse-trace/actions/runs/26904875876", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/epiverse-trace/epiparameter", "_commit": { "id": "291bfd2490cc4c59f002652d3100139c64499107", "author": "Joshua Lambert ", "committer": "Joshua Lambert ", "message": "update WORDLIST\n", "time": 1780507312 }, "_maintainer": { "name": "Joshua W. Lambert", "email": "joshua.lambert@lshtm.ac.uk", "login": "joshwlambert", "bluesky": "@jwlambert.bsky.social", "orcid": "0000-0001-5218-3046", "description": "Software engineer | evolutionary biologist | island biogeographer", "uuid": 46606402 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "cachem", "role": "Imports" }, { "package": "checkmate", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "distcrete", "role": "Imports" }, { "package": "distributional", "role": "Imports" }, { "package": "epiparameterDB", "version": ">= 0.1.0.9000", "role": "Imports" }, { "package": "graphics", "role": "Imports" }, { "package": "httr2", "role": "Imports" }, { "package": "pillar", "role": "Imports" }, { "package": "rlang", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tools", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "bookdown", "role": "Suggests" }, { "package": "DT", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "RColorBrewer", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.1.5", "role": "Suggests" }, { "package": "vdiffr", "version": ">= 1.0.7", "role": "Suggests" }, { "package": "visNetwork", "role": "Suggests" } ], "_owner": "epiverse-trace", "_selfowned": true, "_usedby": 1, "_updates": [ { "week": "2025-34", "n": 1 }, { "week": "2025-35", "n": 5 }, { "week": "2025-46", "n": 8 }, { "week": "2026-02", "n": 9 }, { "week": "2026-06", "n": 1 }, { "week": "2026-10", "n": 1 }, { "week": "2026-16", "n": 1 }, { "week": "2026-18", "n": 29 }, { "week": "2026-19", "n": 20 }, { "week": "2026-23", "n": 29 } ], "_tags": [], "_topics": [ "data-access", "data-package", "epidemiology", "epiverse", "probability-distribution" ], "_stars": 37, "_contributors": [ { "user": "joshwlambert", "count": 1235, "uuid": 46606402 }, { "user": "bisaloo", "count": 29, "uuid": 10783929 }, { "user": "adamkucharski", "count": 28, "uuid": 8329046 }, { "user": "carmentamayo", "count": 7, "uuid": 114071268 }, { "user": "sbfnk", "count": 5, "uuid": 1156307 }, { "user": "chartgerink", "count": 4, "uuid": 2946344 }, { "user": "cm401", "count": 2, "uuid": 26151931 }, { "user": "jamesmbaazam", "count": 2, "uuid": 43169674 }, { "user": "avallecam", "count": 1, "uuid": 21230390 }, { "user": "maelle", "count": 1, "uuid": 8360597 }, { "user": "pitmonticone", "count": 1, "uuid": 38562595 } ], "_userbio": { "uuid": 101338582, "type": "organization", "name": "Epiverse-TRACE" }, "_downloads": { "count": 290, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/epiparameter" }, "_devurl": "https://github.com/epiverse-trace/epiparameter", "_pkgdown": "https://epiverse-trace.github.io/epiparameter/", "_searchresults": 168, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/epiparameter.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/epiverse-trace/epiparameter", "_realowner": "epiverse-trace", "_cranurl": true, "_releases": [ { "version": "0.4.0", "date": "2025-01-08" }, { "version": "0.4.1", "date": "2025-01-24" } ], "_exports": [ "as_epiparameter", "assert_epiparameter", "calc_disc_dist_quantile", "cdf", "convert_params_to_summary_stats", "convert_summary_stats_to_params", "create_citation", "create_metadata", "create_method_assess", "create_prob_distribution", "create_region", "create_summary_stats", "create_uncertainty", "discretise", "discretize", "epiparameter", "epiparameter_db", "extract_param", "generate", "get_citation", "get_parameters", "is_continuous", "is_epiparameter", "is_epiparameter_params", "is_parameterised", "is_parameterized", "is_truncated", "parameter_tbl", "test_epiparameter" ], "_datasets": [ { "name": "epireview_core_cols", "title": "A vector of 'character' strings with the core column names of the epidemiological parameter data exported by the 'epireview' R package.", "object": "epireview_core_cols", "class": [ "character" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "aggregate.multi_epiparameter", "title": "Aggregate multiple objects into a single object.", "topics": [ "aggregate.multi_epiparameter" ] }, { "page": "as_epiparameter", "title": "Convert to an object", "topics": [ "as_epiparameter" ] }, { "page": "as_epiparameter.data.frame", "title": "Convert to an object", "topics": [ "as_epiparameter.data.frame" ] }, { "page": "as.data.frame.epiparameter", "title": "'as.data.frame()' method for class", "topics": [ "as.data.frame.epiparameter" ] }, { "page": "as.data.frame.multi_epiparameter", "title": "'as.data.frame()' method for class", "topics": [ "as.data.frame.multi_epiparameter" ] }, { "page": "as.function.epiparameter", "title": "'as.function()' method for class", "topics": [ "as.function.epiparameter" ] }, { "page": "assert_epiparameter", "title": "Assert an object is a valid object", "topics": [ "assert_epiparameter" ] }, { "page": "c.epiparameter", "title": "'c()' method for class", "topics": [ "c.epiparameter", "c.multi_epiparameter" ] }, { "page": "calc_disc_dist_quantile", "title": "Calculate the quantiles of a probability distribution based on the vector of probabilities and time data (e.g. time since infection)", "topics": [ "calc_disc_dist_quantile" ] }, { "page": "convert_params_to_summary_stats", "title": "Convert the parameter(s) of a distribution to summary statistics", "topics": [ "convert_params_to_summary_stats", "convert_params_to_summary_stats.character", "convert_params_to_summary_stats.epiparameter" ] }, { "page": "convert_summary_stats_to_params", "title": "Convert the summary statistics of a distribution to parameters", "topics": [ "convert_summary_stats_to_params", "convert_summary_stats_to_params.character", "convert_summary_stats_to_params.epiparameter" ] }, { "page": "create_citation", "title": "Create a citation for an object", "topics": [ "create_citation" ] }, { "page": "create_metadata", "title": "Specify metadata associated with data set", "topics": [ "create_metadata" ] }, { "page": "create_method_assess", "title": "Specify methodological aspects of distribution fitting", "topics": [ "create_method_assess" ] }, { "page": "create_prob_distribution", "title": "Create a distribution object", "topics": [ "create_prob_distribution" ] }, { "page": "create_region", "title": "Specify the geography of the data entry", "topics": [ "create_region" ] }, { "page": "create_summary_stats", "title": "Specify reported summary statistics", "topics": [ "create_summary_stats" ] }, { "page": "create_uncertainty", "title": "Specify distribution parameter uncertainty", "topics": [ "create_uncertainty" ] }, { "page": "discretise", "title": "Discretises a continuous distribution in an object", "topics": [ "discretise", "discretise.default", "discretise.epiparameter", "discretize" ] }, { "page": "epiparameter", "title": "Create an object", "topics": [ "epiparameter" ] }, { "page": "epiparameter_db", "title": "Create object(s) directly from the epiparameter library (database)", "topics": [ "epiparameter_db" ] }, { "page": "epiparameter_default_options", "title": "Package options", "topics": [ "epiparameter_default_options" ] }, { "page": "epiparameter_distribution_functions", "title": "PDF, CDF, PMF, quantiles and random number generation for objects", "topics": [ "cdf.epiparameter", "density.epiparameter", "epiparameter_distribution_functions", "generate.epiparameter", "quantile.epiparameter" ] }, { "page": "epireview_core_cols", "title": "A vector of 'character' strings with the core column names of the epidemiological parameter data exported by the 'epireview' R package.", "topics": [ "epireview_core_cols" ] }, { "page": "extract_param", "title": "Calculate the parameters of a parametric probability distribution from reported values of percentiles, or median and range", "topics": [ "extract_param" ] }, { "page": "family.epiparameter", "title": "Family method for the class", "topics": [ "family.epiparameter" ] }, { "page": "format.epiparameter", "title": "Format method for class", "topics": [ "format.epiparameter" ] }, { "page": "get_citation", "title": "Get citation from an object", "topics": [ "get_citation" ] }, { "page": "get_citation.epiparameter", "title": "Get citation from an object", "topics": [ "get_citation.epiparameter" ] }, { "page": "get_citation.multi_epiparameter", "title": "Get citation from a list of objects", "topics": [ "get_citation.multi_epiparameter" ] }, { "page": "get_parameters", "title": "Get parameters from an object", "topics": [ "get_parameters" ] }, { "page": "get_parameters.epiparameter", "title": "Get parameters from an object", "topics": [ "get_parameters.epiparameter", "get_parameters.multi_epiparameter" ] }, { "page": "is_continuous", "title": "Check if distribution in is continuous", "topics": [ "is_continuous" ] }, { "page": "is_epiparameter", "title": "Check object is an ", "topics": [ "is_epiparameter" ] }, { "page": "is_epiparameter_params", "title": "Check whether the vector of parameters for the probability distribution are in the set of possible parameters used in the epiparameter package", "topics": [ "is_epiparameter_params" ] }, { "page": "is_parameterised", "title": "Check if or list of objects contains a distribution and distribution parameters", "topics": [ "is_parameterised", "is_parameterised.epiparameter", "is_parameterised.multi_epiparameter", "is_parameterized" ] }, { "page": "is_truncated", "title": "Check if distribution in is truncated", "topics": [ "is_truncated" ] }, { "page": "lines.epiparameter", "title": "'lines()' method for class", "topics": [ "lines.epiparameter" ] }, { "page": "mean.epiparameter", "title": "Mean method for class", "topics": [ "mean.epiparameter" ] }, { "page": "parameter_tbl", "title": "Table of epidemiological distributions", "topics": [ "parameter_tbl" ] }, { "page": "plot.epiparameter", "title": "Plot method for class", "topics": [ "plot.epiparameter" ] }, { "page": "plot.multi_epiparameter", "title": "'plot()' method for class", "topics": [ "plot.multi_epiparameter" ] }, { "page": "print.epiparameter", "title": "Print method for class", "topics": [ "print.epiparameter" ] }, { "page": "print.multi_epiparameter", "title": "Print method for class", "topics": [ "print.multi_epiparameter" ] }, { "page": "test_epiparameter", "title": "Test whether an object is a valid object", "topics": [ "test_epiparameter" ] } ], "_pkglogo": "https://github.com/epiverse-trace/epiparameter/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/epiverse-trace/epiparameter/raw/HEAD/README.md", "_rundeps": [ "askpass", "backports", "cachem", "checkmate", "cli", "curl", "distcrete", "distributional", "epiparameterDB", "fastmap", "generics", "glue", "httr2", "lifecycle", "magrittr", "numDeriv", "openssl", "pillar", "R6", "rappdirs", "rlang", "sys", "utf8", "vctrs", "withr" ], "_vignettes": [ { "source": "database.Rmd", "filename": "database.html", "title": "Current database", "engine": "knitr::rmarkdown", "headings": [], "created": "2024-05-23 15:12:39", "modified": "2024-10-09 09:50:09", "commits": 11 }, { "source": "data_protocol.Rmd", "filename": "data_protocol.html", "title": "Data Collation and Synthesis Protocol", "engine": "knitr::rmarkdown", "headings": [ "About the package", "Objective of", "Contributing to the package", "Scope of package", "Guide to identifying distributions in the literature", "Guide to data refinement once sources identified", "Guide to extracting parameters", "Data quality assessment in", "Guide to the {epiparameter} review process", "Updating parameters in the database", "Database of excluded papers", "References" ], "created": "2023-03-02 16:52:56", "modified": "2025-01-08 15:55:59", "commits": 24 }, { "source": "design_principles.Rmd", "filename": "design_principles.html", "title": "Design Principles for {epiparameter}", "engine": "knitr::rmarkdown", "headings": [ "Scope", "Output", "Package architecture", "Design decisions", "Dependencies", "Contribute" ], "created": "2023-11-15 13:20:13", "modified": "2024-11-22 13:24:55", "commits": 15 }, { "source": "epiparameter.Rmd", "filename": "epiparameter.html", "title": "Getting Started with {epiparameter}", "engine": "knitr::rmarkdown", "headings": [ "Use case", "Library of epidemiological parameters", "Single set of epidemiological parameters", "Benefit of ", "Subsetting database", "Distribution functions", "Plotting epidemiological distributions", "Accessors", "Parameter conversion and extraction", "Conversion", "Extraction", "Adding library entries and contributing to" ], "created": "2022-10-18 15:52:24", "modified": "2024-10-09 09:50:09", "commits": 58 }, { "source": "extract_convert.Rmd", "filename": "extract_convert.html", "title": "Parameter extraction and conversion in {epiparameter}", "engine": "knitr::rmarkdown", "headings": [ "Conversion versus extraction", "Conversions", "Conversion functions", "Gamma distribution", "Using a character string to name distribution", "Using an ", "Lognormal distribution", "Weibull distribution", "Negative binomial distribution", "Geometric distribution", "Extraction", "Use cases", "Assuming distributions", "References" ], "created": "2023-04-27 15:09:12", "modified": "2024-10-09 09:50:09", "commits": 23 } ], "_score": 9.668572269184558, "_indexed": true, "_nocasepkg": "epiparameter", "_universes": [ "epiverse-trace", "joshwlambert" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.4.1.9000", "date": "2026-06-03T18:35:32.000Z", "distro": "noble", "commit": "291bfd2490cc4c59f002652d3100139c64499107", "fileid": "afe2dca078057b08cc61ccecfb70de582b841858510440eda3618c0914396b3c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiverse-trace/actions/runs/26904875876" }, { "r": "4.6.0", "os": "linux", "version": "0.4.1.9000", "date": "2026-06-03T18:35:32.000Z", "distro": "noble", "commit": "291bfd2490cc4c59f002652d3100139c64499107", "fileid": "3a244f97c0409f1f9e160a5f2f4d0daae91e3e4c2a71741706e9255d16c77924", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiverse-trace/actions/runs/26904875876" }, { "r": "4.5.3", "os": "mac", "version": "0.4.1.9000", "date": "2026-06-03T18:35:34.000Z", "commit": "291bfd2490cc4c59f002652d3100139c64499107", "fileid": "36202e9b06cb1b1631193d28725f47bffd0d11e76658527ca9dfad9daaf93807", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiverse-trace/actions/runs/26904875876" }, { "r": "4.6.0", "os": "mac", "version": "0.4.1.9000", "date": "2026-06-03T18:38:12.000Z", "commit": "291bfd2490cc4c59f002652d3100139c64499107", "fileid": "700a270486ac37a4a917a966f39001e7bb9ec5fae9999f3f8a89bab275782fe1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiverse-trace/actions/runs/26904875876" }, { "r": "4.6.0", "os": "wasm", "version": "0.4.1.9000", "date": "2026-06-03T18:35:26.000Z", "commit": "291bfd2490cc4c59f002652d3100139c64499107", "fileid": "fd83c7e6601f0f2ec6c5d693c178a3a9d9ffac42931a352391e11a2df6202f33", "status": "success", "buildurl": "https://github.com/r-universe/epiverse-trace/actions/runs/26904875876" }, { "r": "4.7.0", "os": "win", "version": "0.4.1.9000", "date": "2026-06-03T18:34:44.000Z", "commit": "291bfd2490cc4c59f002652d3100139c64499107", "fileid": "95bcb0669d4f9d99409fb6809585936c31e63ff27cf9b7d569aa0da16a4284f3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiverse-trace/actions/runs/26904875876" }, { "r": "4.5.3", "os": "win", "version": "0.4.1.9000", "date": "2026-06-03T18:34:45.000Z", "commit": "291bfd2490cc4c59f002652d3100139c64499107", "fileid": "eea8701a9d4d34bacfd856be0c6e2641246b6adf420fad50b30fddd2f35e2453", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiverse-trace/actions/runs/26904875876" }, { "r": "4.6.0", "os": "win", "version": "0.4.1.9000", "date": "2026-06-03T18:34:46.000Z", "commit": "291bfd2490cc4c59f002652d3100139c64499107", "fileid": "72ef694db7b76245e4e7e4fe944943ff28af4986c9374838a8c85a1660dfe9e5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/epiverse-trace/actions/runs/26904875876" } ] }