{
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"Package": "incidence",
"Type": "Package",
"Title": "Compute, Handle, Plot and Model Incidence of Dated Events",
"Version": "1.7.6",
"Authors@R": "c(\nperson(\"Thibaut\", \"Jombart\", role = c(\"aut\"), email = \"thibautjombart@gmail.com\"),\nperson(\"Zhian N.\", \"Kamvar\", role = \"aut\", email = \"zkamvar@gmail.com\",\ncomment = c(ORCID = \"0000-0003-1458-7108\")),\nperson(\"Rich\", \"FitzJohn\", role = \"aut\", email = \"rich.fitzjohn@gmail.com\"),\nperson(\"Tim\", \"Taylor\", role = \"cre\", email = \"tim.taylor@hiddenelephants.co.uk\",\ncomment = c(ORCID = \"0000-0002-8587-7113\")),\nperson(\"Jun\", \"Cai\", role = \"ctb\", email = \"cai-j12@mails.tsinghua.edu.cn\",\ncomment = c(ORCID = \"0000-0001-9495-1226\")),\nperson(\"Sangeeta\", \"Bhatia\", role = \"ctb\", email = \"sangeetabhatia03@gmail.com\"),\nperson(\"Jakob\", \"Schumacher\", role = \"ctb\"),\nperson(\"Juliet R.C.\", \"Pulliam\", role = \"ctb\", email = \"pulliam@sun.ac.za\",\ncomment = c(ORCID = \"0000-0003-3314-8223\"))\n)",
"Description": "Provides functions and classes to compute, handle and\nvisualise incidence from dated events for a defined time\ninterval. Dates can be provided in various standard formats.\nThe class 'incidence' is used to store computed incidence and\ncan be easily manipulated, subsetted, and plotted. In addition,\nlog-linear models can be fitted to 'incidence' objects using\n'fit'. This package is part of the RECON\n() toolkit for outbreak\nanalysis.",
"Encoding": "UTF-8",
"License": "MIT + file LICENSE",
"URL": "https://www.repidemicsconsortium.org/incidence/",
"BugReports": "https://github.com/reconhub/incidence/issues",
"RoxygenNote": "7.3.2",
"VignetteBuilder": "knitr",
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"Repository": "https://reconhub.r-universe.dev",
"Date/Publication": "2025-06-19 21:25:56 UTC",
"RemoteUrl": "https://github.com/reconhub/incidence",
"RemoteRef": "HEAD",
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"User": "root"
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"Author": "Thibaut Jombart [aut],\nZhian N. Kamvar [aut] (ORCID: ),\nRich FitzJohn [aut],\nTim Taylor [cre] (ORCID: ),\nJun Cai [ctb] (ORCID: ),\nSangeeta Bhatia [ctb],\nJakob Schumacher [ctb],\nJuliet R.C. Pulliam [ctb] (ORCID:\n)",
"Maintainer": "Tim Taylor ",
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"_user": "reconhub",
"_type": "src",
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"_published": "2026-06-02T17:24:13.306Z",
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"_status": "success",
"_host": "GitHub-Actions",
"_upstream": "https://github.com/reconhub/incidence",
"_commit": {
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"author": "Tim Taylor ",
"committer": "Tim Taylor ",
"message": "CRAN: submission + site rebuild\n",
"time": 1750368356
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"_maintainer": {
"name": "Tim Taylor",
"email": "tim.taylor@hiddenelephants.co.uk",
"login": "timtaylor",
"description": "\n",
"uuid": 43499035,
"orcid": "0000-0002-8587-7113"
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"_owner": "reconhub",
"_selfowned": true,
"_usedby": 11,
"_updates": [
{
"week": "2025-25",
"n": 5
}
],
"_tags": [],
"_topics": [
"outbreak"
],
"_stars": 57,
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"_userbio": {
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"type": "organization",
"name": "R Epidemics Consortium",
"description": "Consortium for epidemics analysis and outbreak response using R"
},
"_downloads": {
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"source": "https://cranlogs.r-pkg.org/downloads/total/last-month/incidence"
},
"_mentions": 9,
"_devurl": "https://github.com/reconhub/incidence",
"_pkgdown": "https://www.repidemicsconsortium.org/incidence/",
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"_assets": [
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"extra/citation.html",
"extra/citation.json",
"extra/citation.txt",
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"extra/NEWS.html",
"extra/NEWS.txt",
"extra/readme.html",
"extra/readme.md",
"manual.pdf"
],
"_homeurl": "https://github.com/reconhub/incidence",
"_realowner": "reconhub",
"_cranurl": true,
"_releases": [
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"date": "2016-11-03"
},
{
"version": "1.0.1",
"date": "2016-11-22"
},
{
"version": "1.1.0",
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{
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{
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{
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"date": "2018-11-30"
},
{
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"date": "2019-01-15"
},
{
"version": "1.7.0",
"date": "2019-03-14"
},
{
"version": "1.7.1",
"date": "2020-03-25"
},
{
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"date": "2020-07-24"
},
{
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{
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"date": "2024-05-31"
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],
"_exports": [
"add_incidence_fit",
"as.incidence",
"bootstrap",
"cumulate",
"estimate_peak",
"find_peak",
"fit",
"fit_optim_split",
"get_counts",
"get_dates",
"get_fit",
"get_info",
"get_interval",
"get_n",
"get_timespan",
"group_names",
"group_names<-",
"incidence",
"incidence_pal1",
"incidence_pal1_dark",
"incidence_pal1_light",
"make_breaks",
"pool",
"scale_x_incidence"
],
"_help": [
{
"page": "conversions",
"title": "Conversion of incidence objects",
"topics": [
"as.data.frame.incidence",
"as.incidence",
"as.incidence.data.frame",
"as.incidence.matrix",
"as.incidence.numeric"
]
},
{
"page": "bootstrap",
"title": "Bootstrap incidence time series",
"topics": [
"bootstrap"
]
},
{
"page": "cumulate",
"title": "Compute cumulative 'incidence'",
"topics": [
"cumulate",
"cumulate.default",
"cumulate.incidence"
]
},
{
"page": "accessors",
"title": "Access various elements of an incidence object",
"topics": [
"dim.incidence",
"get_interval",
"get_interval.default",
"get_interval.incidence",
"get_n",
"get_n.default",
"get_n.incidence",
"get_timespan",
"get_timespan.default",
"get_timespan.incidence"
]
},
{
"page": "estimate_peak",
"title": "Estimate the peak date of an incidence curve using bootstrap",
"topics": [
"estimate_peak"
]
},
{
"page": "find_peak",
"title": "Find the peak date of an incidence curve",
"topics": [
"find_peak"
]
},
{
"page": "fit",
"title": "Fit exponential models to incidence data",
"topics": [
"fit",
"fit_optim_split",
"print.incidence_fit",
"print.incidence_fit_list"
]
},
{
"page": "get_counts",
"title": "Get counts from an incidence object",
"topics": [
"get_counts",
"get_counts.incidence"
]
},
{
"page": "get_dates",
"title": "Retrieve dates from an incidence object",
"topics": [
"get_dates",
"get_dates.default",
"get_dates.incidence"
]
},
{
"page": "get_fit",
"title": "Accessors for 'incidence_fit' objects",
"topics": [
"get_fit",
"get_fit.incidence_fit",
"get_fit.incidence_fit_list",
"get_info",
"get_info.incidence_fit",
"get_info.incidence_fit_list"
]
},
{
"page": "group_names",
"title": "extract and set group names",
"topics": [
"group_names",
"group_names.default",
"group_names.incidence",
"group_names<-",
"group_names<-.default",
"group_names<-.incidence",
"`group_names<-`.default"
]
},
{
"page": "incidence",
"title": "Compute incidence of events from a vector of dates.",
"topics": [
"incidence",
"incidence.character",
"incidence.Date",
"incidence.default",
"incidence.integer",
"incidence.numeric",
"incidence.POSIXt",
"print.incidence"
]
},
{
"page": "palettes",
"title": "Color palettes used in incidence",
"topics": [
"incidence_pal1",
"incidence_pal1_dark",
"incidence_pal1_light",
"palettes"
]
},
{
"page": "plot.incidence",
"title": "Plot function for incidence objects",
"topics": [
"add_incidence_fit",
"make_breaks",
"plot.incidence",
"plot.incidence_fit",
"plot.incidence_fit_list",
"scale_x_incidence"
]
},
{
"page": "pool",
"title": "Pool 'incidence' across groups",
"topics": [
"pool"
]
},
{
"page": "subset",
"title": "Subsetting 'incidence' objects",
"topics": [
"\"subset.incidence\"",
"\"[.incidence\"",
"subset.incidence",
"[.incidence"
]
}
],
"_readme": "https://github.com/reconhub/incidence/raw/HEAD/README.md",
"_rundeps": [
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"cli",
"cpp11",
"farver",
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"title": "Conversions to and from the incidence class",
"author": "Thibaut Jombart, Zhian N. Kamvar",
"engine": "knitr::rmarkdown",
"headings": [
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],
"created": "2017-04-03 15:55:23",
"modified": "2020-11-03 17:18:51",
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"The plot.incidence function",
"Default behaviour",
"Changing colors",
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"Using different palettes",
"Specifying colors manually",
"Example 1: changing a single color",
"Example 2: changing several colors (note that naming colors is optional)",
"Example 3: using color to highlight specific groups",
"Useful ggplot2 tweaks",
"Changing dates on the x-axis",
"Changing date format",
"Changing the grid",
"Handling non-ISO weeks",
"Labelling every bin",
"Changing the legend",
"Applying the style of European Programme for Intervention Epidemiology Training (EPIET)",
"Display individual cases"
],
"created": "2016-10-25 08:33:25",
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"title": "Details of the incidence class",
"author": "Thibaut Jombart, Zhian N. Kamvar",
"engine": "knitr::rmarkdown",
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"$dates",
"$counts",
"$timespan",
"$interval",
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],
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"engine": "knitr::rmarkdown",
"headings": [
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"Building an incidence_fit object from scratch",
"Step 1: create the model",
"Step 2: creation of the $info list:",
"Step 3: combine lists and create object",
"Structure of an incidence_fit_list object",
"Example: A tale of two fits",
"Example: Nested incidence_fit"
],
"created": "2018-08-21 13:31:04",
"modified": "2018-11-30 10:08:39",
"commits": 4
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"author": "Thibaut Jombart, Zhian N. Kamvar",
"engine": "knitr::rmarkdown",
"headings": [
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"What does it do?",
"Worked example: simulated Ebola outbreak",
"Loading the data",
"Computing and plotting incidence",
"Handling incidence objects",
"Modelling incidence"
],
"created": "2016-10-17 11:51:17",
"modified": "2024-05-15 10:48:16",
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