{ "_id": "6a23315b530b9bc726bd22ee", "Type": "Package", "Package": "EpiNow2", "Title": "Estimate and Forecast Real-Time Infection Dynamics", "Version": "1.8.0.9000", "Authors@R": "c(person(given = \"Sam\",\nfamily = \"Abbott\",\nrole = c(\"aut\"),\nemail = \"sam.abbott@lshtm.ac.uk\",\ncomment = c(ORCID = \"0000-0001-8057-8037\")),\nperson(given = \"Joel\",\nfamily = \"Hellewell\",\nrole = \"aut\",\nemail = \"joel.hellewell@lshtm.ac.uk\",\ncomment = c(ORCID = \"0000-0003-2683-0849\")),\nperson(given = \"Katharine\",\nfamily = \"Sherratt\",\nrole = \"aut\",\nemail = \"katharine.sherratt@lshtm.ac.uk\"),\nperson(given = \"Katelyn\",\nfamily = \"Gostic\",\nrole = \"aut\",\nemail = \"kgostic@uchicago.edu\"),\nperson(given = \"Joe\",\nfamily = \"Hickson\",\nrole = \"aut\",\nemail = \"joseph.hickson@metoffice.gov.uk\"),\nperson(given = \"Hamada S.\",\nfamily = \"Badr\",\nrole = \"aut\",\nemail = \"badr@jhu.edu\",\ncomment = c(ORCID = \"0000-0002-9808-2344\")),\nperson(given = \"Michael\",\nfamily = \"DeWitt\",\nrole = \"aut\",\nemail = \"me.dewitt.jr@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8940-1967\")),\nperson(given = \"James M.\",\nfamily = \"Azam\",\nrole = \"aut\",\nemail = \"james.azam@lshtm.ac.uk\",\ncomment = c(ORCID = \"0000-0001-5782-7330\")),\nperson(given = \"Adrian\",\nfamily = \"Lison\",\nrole = \"aut\",\nemail = \"adrian.lison@bsse.ethz.ch\",\ncomment = c(ORCID = \"0000-0002-6822-8437\")),\nperson(given = \"Robin\",\nfamily = \"Thompson\",\nrole = \"ctb\",\nemail = \"robin.thompson@lshtm.ac.uk\"),\nperson(given = \"Sophie\",\nfamily = \"Meakin\",\nrole = \"ctb\",\nemail = \"sophie.meakin@lshtm.ac.uk\"),\nperson(given = \"James\",\nfamily = \"Munday\",\nrole = \"ctb\",\nemail = \"james.munday@lshtm.ac.uk\"),\nperson(given = \"Nikos\",\nfamily = \"Bosse\",\nrole = \"ctb\"),\nperson(given = \"Paul\",\nfamily = \"Mee\",\nrole = \"ctb\",\nemail = \"paul.mee@lshtm.ac.uk\"),\nperson(given = \"Peter\",\nfamily = \"Ellis\",\nrole = \"ctb\",\nemail = \"peter.ellis2013nz@gmail.com\"),\nperson(given = \"Pietro\",\nfamily = \"Monticone\",\nrole = \"ctb\",\nemail = \"pietro.monticone@edu.unito.it\"),\nperson(given = \"Lloyd\",\nfamily = \"Chapman\",\nrole = \"ctb\",\nemail = \"lloyd.chapman1@lshtm.ac.uk\"),\nperson(given = \"Andrew\",\nfamily = \"Johnson\",\nrole = \"ctb\",\nemail = \"andrew.johnson@arjohnsonau.com\"),\nperson(given = \"Kaitlyn\",\nfamily = \"Johnson\",\nrole = \"ctb\",\nemail = \"johnsonkaitlyne9@gmail.com\",\ncomment = c(ORCID = \"0000-0001-8011-0012\")),\nperson(given = \"Adam\",\nfamily = \"Howes\",\nrole = \"ctb\",\nemail = \"adamthowes@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2386-4031\")),\nperson(given = \"Sebastian\",\nfamily = \"Funk\",\nrole = c(\"aut\", \"cre\"),\nemail = \"sebastian.funk@lshtm.ac.uk\",\ncomment = c(ORCID = \"0000-0002-2842-3406\"))\n)", "Description": "Estimates the time-varying reproduction number, rate of\nspread, and doubling time using a renewal equation approach\ncombined with Bayesian inference via Stan. Supports Gaussian\nprocess and random walk priors for modelling changes in\ntransmission over time. Accounts for delays between infection\nand observation (incubation period, reporting delays),\nright-truncation in recent data, day-of-week effects, and\nobservation overdispersion. Can estimate relationships between\nprimary and secondary outcomes (e.g., cases to hospitalisations\nor deaths) and forecast both. Runs across multiple regions in\nparallel. Based on Abbott et al. (2020)\n and Gostic et al. (2020)\n.", "License": "MIT + file LICENSE", "URL": "https://epiforecasts.io/EpiNow2/,\nhttps://epiforecasts.io/EpiNow2/dev/,\nhttps://github.com/epiforecasts/EpiNow2", "BugReports": "https://github.com/epiforecasts/EpiNow2/issues", "Additional_repositories": "https://production.r-multiverse.org/2026-03-15", "Biarch": "true", "Config/testthat/edition": "3", "Config/Needs/dev": "covr, here, hexSticker, lintr, magick, pkgdown,\nprecommit, styler, usethis", "Encoding": "UTF-8", "Language": "en-GB", "LazyData": "true", "Roxygen": "list(markdown = TRUE)", "SystemRequirements": "GNU make C++17", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.0.0", "Config/pak/sysreqs": "make", "Repository": "https://epiforecasts.r-universe.dev", "Date/Publication": "2026-06-05 14:39:35 UTC", "RemoteUrl": "https://github.com/epiforecasts/EpiNow2", "RemoteRef": "HEAD", "RemoteSha": "b405f7061811a5b982d2bca638488344de3139d6", "NeedsCompilation": "no", "Packaged": { "Date": "2026-06-05 19:59:46 UTC", "User": "root" }, "Author": "Sam Abbott [aut] (ORCID: ),\nJoel Hellewell [aut] (ORCID: ),\nKatharine Sherratt [aut],\nKatelyn Gostic [aut],\nJoe Hickson [aut],\nHamada S. Badr [aut] (ORCID: ),\nMichael DeWitt [aut] (ORCID: ),\nJames M. Azam [aut] (ORCID: ),\nAdrian Lison [aut] (ORCID: ),\nRobin Thompson [ctb],\nSophie Meakin [ctb],\nJames Munday [ctb],\nNikos Bosse [ctb],\nPaul Mee [ctb],\nPeter Ellis [ctb],\nPietro Monticone [ctb],\nLloyd Chapman [ctb],\nAndrew Johnson [ctb],\nKaitlyn Johnson [ctb] (ORCID: ),\nAdam Howes [ctb] (ORCID: ),\nSebastian Funk [aut, cre] (ORCID:\n)", "Maintainer": "Sebastian Funk ", "MD5sum": "c5e1c2d21082003791502db4a382c97a", "_user": "epiforecasts", "_type": "src", "_file": "EpiNow2_1.8.0.9000.tar.gz", "_fileid": "6de27b2f78916bc362a31efff3e0825fdccc23e7d7fb1c944e5600ada09a3a38", "_filesize": 7324027, "_sha256": "6de27b2f78916bc362a31efff3e0825fdccc23e7d7fb1c944e5600ada09a3a38", "_created": "2026-06-05T19:59:46.000Z", "_published": "2026-06-05T20:28:11.793Z", "_distro": "noble", "_jobs": [ { "job": 79804798882, "time": 676, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7445971284" }, { "job": 79804798860, "time": 651, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7445963314" }, { "job": 79804798899, "time": 709, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7445980349" }, { "job": 79804798881, "time": 701, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7445976895" }, { "job": 79804798885, "time": 540, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7445952646" }, { "job": 79804798978, "time": 833, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7446053543" }, { "job": 79804798895, "time": 351, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7445914041" }, { "job": 79804798975, "time": 896, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7446147117" }, { "job": 79802117684, "time": 1030, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7445771299" }, { "job": 79804798793, "time": 185, "config": "wasm-release", "r": "4.6.0", "check": "FAIL", "artifact": "" }, { "job": 79804798856, "time": 1013, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7446065790" }, { "job": 79804798887, "time": 993, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7446060548" }, { "job": 79804798842, "time": 997, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7446061608" } ], "_buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/epiforecasts/EpiNow2", "_commit": { "id": "b405f7061811a5b982d2bca638488344de3139d6", "author": "Sam Abbott ", "committer": "GitHub ", "message": "Disable caching for R dependencies (#1439)", "time": 1780670375 }, "_maintainer": { "name": "Sebastian Funk", "email": "sebastian.funk@lshtm.ac.uk", "login": "sbfnk", "mastodon": "@sbfnk@fosstodon.org", "bluesky": "@sbfnk.bsky.social", "orcid": "0000-0002-2842-3406", "description": "Professor of Infectious Disease Dynamics at LSHTM. epiforecasts.io", "uuid": 1156307 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5.0", "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": ">= 2.26.0", "role": "LinkingTo" }, { "package": "StanHeaders", "version": ">= 2.26.0", "role": "LinkingTo" }, { "package": "checkmate", "role": "Imports" }, { "package": "cli", "role": "Imports" }, { "package": "data.table", "version": ">= 1.15.0", "role": "Imports" }, { "package": "futile.logger", "version": ">= 1.4", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "lifecycle", "role": "Imports" }, { "package": "lubridate", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "posterior", "role": "Imports" }, { "package": "primarycensored", "role": "Imports" }, { "package": "purrr", "role": "Imports" }, { "package": "R.utils", "version": ">= 2.0.0", "role": "Imports" }, { "package": "Rcpp", "version": ">= 0.12.0", "role": "Imports" }, { "package": "rlang", "version": ">= 0.4.7", "role": "Imports" }, { "package": "rstan", "version": ">= 2.26.0", "role": "Imports" }, { "package": "rstantools", "version": ">= 2.2.0", "role": "Imports" }, { "package": "runner", "role": "Imports" }, { "package": "scales", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "truncnorm", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "cmdstanr", "role": "Suggests" }, { "package": "future", "role": "Suggests" }, { "package": "future.apply", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "parallelly", "role": "Suggests" }, { "package": "progressr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "scoringutils", "role": "Suggests" }, { "package": "spelling", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "withr", "role": "Suggests" } ], "_owner": "epiforecasts", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-23", "n": 5 }, { "week": "2025-26", "n": 2 }, { "week": "2025-28", "n": 3 }, { "week": "2025-33", "n": 1 }, { "week": "2025-37", "n": 1 }, { "week": "2025-41", "n": 1 }, { "week": "2025-43", "n": 3 }, { "week": "2025-44", "n": 8 }, { "week": "2025-45", "n": 4 }, { "week": "2025-46", "n": 12 }, { "week": "2025-47", "n": 5 }, { "week": "2025-48", "n": 5 }, { "week": "2025-49", "n": 4 }, { "week": "2025-50", "n": 4 }, { "week": "2025-51", "n": 12 }, { "week": "2026-02", "n": 1 }, { "week": "2026-03", "n": 3 }, { "week": "2026-04", "n": 9 }, { "week": "2026-05", "n": 8 }, { "week": "2026-06", "n": 20 }, { "week": "2026-07", "n": 1 }, { "week": "2026-08", "n": 1 }, { "week": "2026-09", "n": 1 }, { "week": "2026-11", "n": 3 }, { "week": "2026-14", "n": 1 }, { "week": "2026-15", "n": 1 }, { "week": "2026-16", "n": 1 }, { "week": "2026-19", "n": 3 }, { "week": "2026-20", "n": 3 }, { "week": "2026-21", "n": 4 }, { "week": "2026-23", "n": 11 } ], "_tags": [ { "name": "v1.8.0", "date": "2026-02-05" } ], "_topics": [ "backcalculation", "covid-19", "gaussian-processes", "open-source", "reproduction-number", "stan", "cpp" ], "_stars": 139, "_contributors": [ { "user": "seabbs", "count": 944, "uuid": 20317649 }, { "user": "sbfnk", "count": 472, "uuid": 1156307 }, { "user": "jamesmbaazam", "count": 161, "uuid": 43169674 }, { "user": "joehickson", "count": 57, "uuid": 8492240 }, { "user": "hsbadr", "count": 16, "uuid": 7604200 }, { "user": "pitmonticone", "count": 11, "uuid": 38562595 }, { "user": "seabbs-bot", "count": 10, "uuid": 256795758 }, { "user": "sbfnk-bot", "count": 9, "uuid": 242615673 }, { "user": "ellisp", "count": 5, "uuid": 5740570 }, { "user": "kaitejohnson", "count": 3, "uuid": 94390107 }, { "user": "jdmunday", "count": 3, "uuid": 18169913 }, { "user": "adrian-lison", "count": 2, "uuid": 16266527 }, { "user": "pearsonca", "count": 2, "uuid": 1828039 }, { "user": "bisaloo", "count": 2, "uuid": 10783929 }, { "user": "jallen42", "count": 2, "uuid": 69790602 }, { "user": "adamkucharski", "count": 1, "uuid": 8329046 }, { "user": "avehtari", "count": 1, "uuid": 6705400 }, { "user": "andrjohns", "count": 1, "uuid": 27717896 }, { "user": "claude", "count": 1, "uuid": 81847 }, { "user": "jcken95", "count": 1, "uuid": 57638616 }, { "user": "lloydchapman", "count": 1, "uuid": 22941537 }, { "user": "medewitt", "count": 1, "uuid": 25038837 }, { "user": "nikosbosse", "count": 1, "uuid": 37978797 }, { "user": "sophiemeakin", "count": 1, "uuid": 35970279 }, { "user": "zsusswein", "count": 1, "uuid": 46581799 } ], "_userbio": { "uuid": 54675094, "type": "organization", "name": "Epiforecasts", "description": "Researchers at the London School of Hygiene & Tropical Medicine doing research to forecast infectious diseases and perform real-time analyses." }, "_downloads": { "count": 513, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/EpiNow2" }, "_mentions": 7, "_devurl": "https://github.com/epiforecasts/epinow2", "_pkgdown": "https://epiforecasts.io/EpiNow2/", "_searchresults": 397, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/EpiNow2.html", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://github.com/epiforecasts/epinow2", "_realowner": "epiforecasts", "_cranurl": true, "_releases": [ { "version": "1.1.0", "date": "2020-09-01" }, { "version": "1.2.1", "date": "2020-10-20" }, { "version": "1.3.1", "date": "2020-11-22" }, { "version": "1.3.2", "date": "2020-12-14" }, { "version": "1.3.4", "date": "2023-02-12" }, { "version": "1.3.5", "date": "2023-04-27" }, { "version": "1.4.0", "date": "2023-09-26" }, { "version": "1.5.0", "date": "2024-05-10" }, { "version": "1.5.1", "date": "2024-05-14" }, { "version": "1.5.2", "date": "2024-05-16" }, { "version": "1.6.0", "date": "2024-10-02" }, { "version": "1.6.1", "date": "2024-10-31" }, { "version": "1.7.0", "date": "2025-02-05" }, { "version": "1.7.1", "date": "2025-02-19" }, { "version": "1.8.0", "date": "2026-02-04" } ], "_exports": [ "add_breakpoints", "backcalc_opts", "bootstrapped_dist_fit", "bound_dist", "calc_CrI", "calc_CrIs", "calc_summary_measures", "calc_summary_stats", "clean_nowcasts", "collapse", "convert_to_logmean", "convert_to_logsd", "convolve_and_scale", "delay_opts", "Dirichlet", "discretise", "discretize", "dist_fit", "epinow", "epinow2_cmdstan_model", "estimate_delay", "estimate_dist", "estimate_infections", "estimate_secondary", "estimate_truncation", "Exp", "expose_stan_fns", "extract_CrIs", "extract_inits", "extract_samples", "extract_stan_param", "fill_missing", "filter_leading_zeros", "fix_parameters", "Fixed", "forecast_infections", "forecast_opts", "forecast_secondary", "Gamma", "generation_time_opts", "get_distribution", "get_parameters", "get_pmf", "get_predictions", "get_regional_results", "get_samples", "gp_opts", "growth_to_R", "gt_opts", "is_constrained", "LogNormal", "make_conf", "map_prob_change", "new_dist_spec", "NonParametric", "Normal", "obs_opts", "opts_list", "plot_estimates", "plot_summary", "R_to_growth", "regional_epinow", "regional_runtimes", "regional_summary", "report_plots", "report_summary", "rt_opts", "secondary_opts", "set_dt_single_thread", "setup_default_logging", "setup_future", "setup_logging", "simulate_infections", "simulate_secondary", "stan_laplace_opts", "stan_opts", "stan_pathfinder_opts", "stan_sampling_opts", "stan_vb_opts", "trunc_opts", "update_secondary_args", "Weibull" ], "_datasets": [ { "name": "example_confirmed", "title": "Example Confirmed Case Data Set", "object": "example_confirmed", "class": [ "data.table", "data.frame" ], "fields": [ "date", "confirm" ], "rows": 130, "table": true, "tojson": true }, { "name": "example_generation_time", "title": "Example generation time", "object": "example_generation_time", "class": [ "dist_spec", "list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_incubation_period", "title": "Example incubation period", "object": "example_incubation_period", "class": [ "dist_spec", "list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_reporting_delay", "title": "Example reporting delay", "object": "example_reporting_delay", "class": [ "dist_spec", "list" ], "fields": [], "table": false, "tojson": true }, { "name": "example_truncated", "title": "Example Case Data Set with Truncation", "object": "example_truncated", "class": [ "list" ], "fields": [], "table": true, "tojson": true } ], "_help": [ { "page": "plus-.dist_spec", "title": "Creates a delay distribution as the sum of two other delay distributions.", "topics": [ "+.dist_spec" ] }, { "page": "equals-.dist_spec", "title": "Compares two delay distributions", "topics": [ "!=.dist_spec", "==.dist_spec" ] }, { "page": "add_breakpoints", "title": "Add breakpoints to certain dates in a data set.", "topics": [ "add_breakpoints" ] }, { "page": "apply_zero_threshold", "title": "Convert zero case counts to 'NA' (missing) if the 7-day average is above a threshold.", "topics": [ "apply_zero_threshold" ] }, { "page": "as_forecast_sample", "title": "Convert EpiNow2 model output to a 'forecast_sample' object", "topics": [ "as_forecast_sample", "as_forecast_sample.epinow", "as_forecast_sample.estimate_infections", "as_forecast_sample.estimate_truncation", "as_forecast_sample.forecast_secondary" ] }, { "page": "backcalc_opts", "title": "Back Calculation Options", "topics": [ "backcalc_opts" ] }, { "page": "bootstrapped_dist_fit", "title": "Fit a Subsampled Bootstrap to Integer Values and Summarise Distribution Parameters", "topics": [ "bootstrapped_dist_fit" ] }, { "page": "bound_dist", "title": "Define bounds of a ", "topics": [ "bound_dist" ] }, { "page": "c.dist_spec", "title": "Combines multiple delay distributions for further processing", "topics": [ "c.dist_spec" ] }, { "page": "calc_CrI", "title": "Calculate Credible Interval", "topics": [ "calc_CrI" ] }, { "page": "calc_CrIs", "title": "Calculate Credible Intervals", "topics": [ "calc_CrIs" ] }, { "page": "calc_summary_measures", "title": "Calculate All Summary Measures", "topics": [ "calc_summary_measures" ] }, { "page": "calc_summary_stats", "title": "Calculate Summary Statistics", "topics": [ "calc_summary_stats" ] }, { "page": "clean_nowcasts", "title": "Clean Nowcasts for a Supplied Date", "topics": [ "clean_nowcasts" ] }, { "page": "clean_regions", "title": "Clean Regions", "topics": [ "clean_regions" ] }, { "page": "collapse", "title": "Collapse nonparametric distributions in a ", "topics": [ "collapse", "collapse.dist_spec" ] }, { "page": "convert_to_logmean", "title": "Convert mean and sd to log mean for a log normal distribution", "topics": [ "convert_to_logmean" ] }, { "page": "convert_to_logsd", "title": "Convert mean and sd to log standard deviation for a log normal distribution", "topics": [ "convert_to_logsd" ] }, { "page": "convolve_and_scale", "title": "Convolve and scale a time series", "topics": [ "convolve_and_scale" ] }, { "page": "delay_opts", "title": "Delay Distribution Options", "topics": [ "delay_opts" ] }, { "page": "discretise", "title": "Discretise a ", "topics": [ "discretise", "discretise.dist_spec", "discretize" ] }, { "page": "dist_fit", "title": "Fit an Integer Adjusted Exponential, Gamma or Lognormal distributions", "topics": [ "dist_fit" ] }, { "page": "Distributions", "title": "Probability distributions", "topics": [ "Dirichlet", "Distributions", "Exp", "Fixed", "Gamma", "LogNormal", "NonParametric", "Normal", "Weibull" ] }, { "page": "epinow", "title": "Real-time Rt Estimation, Forecasting and Reporting", "topics": [ "epinow" ] }, { "page": "epinow2_cmdstan_model", "title": "Load and compile an EpiNow2 cmdstanr model", "topics": [ "epinow2_cmdstan_model" ] }, { "page": "estimate_delay", "title": "Estimate a Delay Distribution", "topics": [ "estimate_delay" ] }, { "page": "estimate_dist", "title": "Estimate a delay distribution using primarycensored", "topics": [ "estimate_dist" ] }, { "page": "estimate_infections", "title": "Estimate Infections, the Time-Varying Reproduction Number and the Rate of Growth", "topics": [ "estimate_infections" ] }, { "page": "estimate_secondary", "title": "Estimate a Secondary Observation from a Primary Observation", "topics": [ "estimate_secondary" ] }, { "page": "estimate_truncation", "title": "Estimate truncation of observed data", "topics": [ "estimate_truncation" ] }, { "page": "example_confirmed", "title": "Example Confirmed Case Data Set", "topics": [ "example_confirmed" ] }, { "page": "example_generation_time", "title": "Example generation time", "topics": [ "example_generation_time" ] }, { "page": "example_incubation_period", "title": "Example incubation period", "topics": [ "example_incubation_period" ] }, { "page": "example_reporting_delay", "title": "Example reporting delay", "topics": [ "example_reporting_delay" ] }, { "page": "example_truncated", "title": "Example Case Data Set with Truncation", "topics": [ "example_truncated" ] }, { "page": "expose_stan_fns", "title": "Expose internal package stan functions in R", "topics": [ "expose_stan_fns" ] }, { "page": "extract_CrIs", "title": "Extract Credible Intervals Present", "topics": [ "extract_CrIs" ] }, { "page": "extract_inits", "title": "Generate initial conditions from a Stan fit", "topics": [ "extract_inits" ] }, { "page": "extract_samples", "title": "Extract all samples from a stan fit", "topics": [ "extract_samples" ] }, { "page": "extract_stan_param", "title": "Extract a parameter summary from a Stan object", "topics": [ "extract_stan_param" ] }, { "page": "fill_missing", "title": "Fill missing data in a data set to prepare it for use within the package", "topics": [ "fill_missing" ] }, { "page": "filter_leading_zeros", "title": "Filter leading zeros from a data set.", "topics": [ "filter_leading_zeros" ] }, { "page": "filter_opts", "title": "Filter Options for a Target Region", "topics": [ "filter_opts" ] }, { "page": "fix_parameters", "title": "Fix the parameters of a ", "topics": [ "fix_parameters", "fix_parameters.dist_spec" ] }, { "page": "forecast_infections", "title": "Forecast infections from a given fit and trajectory of the time-varying reproduction number", "topics": [ "forecast_infections" ] }, { "page": "forecast_opts", "title": "Forecast options", "topics": [ "forecast_opts" ] }, { "page": "forecast_secondary", "title": "Forecast Secondary Observations Given a Fit from estimate_secondary", "topics": [ "forecast_secondary" ] }, { "page": "get_distribution", "title": "Get the distribution of a ", "topics": [ "get_distribution" ] }, { "page": "get_parameters", "title": "Get parameters from distributions or fitted models", "topics": [ "get_parameters", "get_parameters.dist_spec", "get_parameters.epinowfit", "get_parameters.estimate_dist" ] }, { "page": "get_pmf", "title": "Get the probability mass function of a nonparametric distribution", "topics": [ "get_pmf" ] }, { "page": "get_predictions", "title": "Get predictions from a fitted model", "topics": [ "get_predictions", "get_predictions.estimate_infections", "get_predictions.estimate_secondary", "get_predictions.estimate_truncation", "get_predictions.forecast_infections", "get_predictions.forecast_secondary" ] }, { "page": "get_regional_results", "title": "Get Combined Regional Results", "topics": [ "get_regional_results" ] }, { "page": "get_samples", "title": "Get posterior samples from a fitted model", "topics": [ "get_samples", "get_samples.epinow", "get_samples.estimate_infections", "get_samples.estimate_secondary", "get_samples.estimate_truncation", "get_samples.forecast_infections", "get_samples.forecast_secondary" ] }, { "page": "gp_opts", "title": "Approximate Gaussian Process Settings", "topics": [ "gp_opts" ] }, { "page": "growth_to_R", "title": "Convert Growth Rates to Reproduction numbers.", "topics": [ "growth_to_R" ] }, { "page": "generation_time_opts", "title": "Generation Time Distribution Options", "topics": [ "generation_time_opts", "gt_opts" ] }, { "page": "is_constrained", "title": "Check if a is constrained, i.e. has a finite maximum or nonzero CDF cutoff.", "topics": [ "is_constrained", "is_constrained.dist_spec" ] }, { "page": "make_conf", "title": "Format Credible Intervals", "topics": [ "make_conf" ] }, { "page": "map_prob_change", "title": "Categorise the Probability of Change for Rt", "topics": [ "map_prob_change" ] }, { "page": "max.dist_spec", "title": "Returns the maximum of one or more delay distribution", "topics": [ "max.dist_spec" ] }, { "page": "mean.dist_spec", "title": "Returns the mean of one or more delay distribution", "topics": [ "mean.dist_spec" ] }, { "page": "new_dist_spec", "title": "Internal function for generating a 'dist_spec' given parameters and a distribution.", "topics": [ "new_dist_spec" ] }, { "page": "obs_opts", "title": "Observation Model Options", "topics": [ "obs_opts" ] }, { "page": "opts_list", "title": "Forecast optiong", "topics": [ "opts_list" ] }, { "page": "plot_CrIs", "title": "Plot EpiNow2 Credible Intervals", "topics": [ "plot_CrIs" ] }, { "page": "plot_estimates", "title": "Plot Estimates", "topics": [ "plot_estimates" ] }, { "page": "plot_summary", "title": "Plot a Summary of the Latest Results", "topics": [ "plot_summary" ] }, { "page": "plot.dist_spec", "title": "Plot PMF and CDF for a dist_spec object", "topics": [ "plot.dist_spec" ] }, { "page": "plot.estimate_infections", "title": "Plot method for estimate_infections", "topics": [ "plot.estimate_infections" ] }, { "page": "plot.estimate_secondary", "title": "Plot method for estimate_secondary", "topics": [ "plot.estimate_secondary" ] }, { "page": "plot.estimate_truncation", "title": "Plot method for estimate_truncation", "topics": [ "plot.estimate_truncation" ] }, { "page": "plot.forecast_infections", "title": "Plot method for forecast_infections", "topics": [ "plot.forecast_infections" ] }, { "page": "plot.forecast_secondary", "title": "Plot method for forecast_secondary objects", "topics": [ "plot.forecast_secondary" ] }, { "page": "print.dist_spec", "title": "Prints the parameters of one or more delay distributions", "topics": [ "print.dist_spec" ] }, { "page": "print.epinowfit", "title": "Print information about an object that has resulted from a model fit.", "topics": [ "print.epinowfit" ] }, { "page": "R_to_growth", "title": "Convert Reproduction Numbers to Growth Rates", "topics": [ "R_to_growth" ] }, { "page": "regional_epinow", "title": "Real-time Rt Estimation, Forecasting and Reporting by Region", "topics": [ "regional_epinow" ] }, { "page": "regional_summary", "title": "Regional Summary Output", "topics": [ "regional_summary" ] }, { "page": "report_plots", "title": "Report plots", "topics": [ "report_plots" ] }, { "page": "report_summary", "title": "Provide Summary Statistics for Estimated Infections and Rt", "topics": [ "report_summary" ] }, { "page": "rt_opts", "title": "Time-Varying Reproduction Number Options", "topics": [ "rt_opts" ] }, { "page": "run_region", "title": "Run epinow with Regional Processing Code", "topics": [ "run_region" ] }, { "page": "secondary_opts", "title": "Secondary Reports Options", "topics": [ "secondary_opts" ] }, { "page": "setup_default_logging", "title": "Setup Default Logging", "topics": [ "setup_default_logging" ] }, { "page": "setup_future", "title": "Set up Future Backend", "topics": [ "setup_future" ] }, { "page": "setup_logging", "title": "Setup Logging", "topics": [ "setup_logging" ] }, { "page": "simulate_infections", "title": "Simulate infections using the renewal equation", "topics": [ "simulate_infections" ] }, { "page": "simulate_secondary", "title": "Simulate secondary observations from primary observations", "topics": [ "simulate_secondary" ] }, { "page": "stan_laplace_opts", "title": "Stan Laplace algorithm Options", "topics": [ "stan_laplace_opts" ] }, { "page": "stan_opts", "title": "Stan Options", "topics": [ "stan_opts" ] }, { "page": "stan_pathfinder_opts", "title": "Stan pathfinder algorithm Options", "topics": [ "stan_pathfinder_opts" ] }, { "page": "stan_sampling_opts", "title": "Stan Sampling Options", "topics": [ "stan_sampling_opts" ] }, { "page": "stan_vb_opts", "title": "Stan Variational Bayes Options", "topics": [ "stan_vb_opts" ] }, { "page": "summary.epinow", "title": "Summary output from epinow", "topics": [ "summary", "summary.epinow" ] }, { "page": "summary.estimate_dist", "title": "Summarise results from estimate_dist", "topics": [ "summary.estimate_dist" ] }, { "page": "summary.estimate_infections", "title": "Summary output from estimate_infections", "topics": [ "summary.estimate_infections" ] }, { "page": "summary.estimate_secondary", "title": "Summarise results from estimate_secondary", "topics": [ "summary.estimate_secondary" ] }, { "page": "summary.estimate_truncation", "title": "Summarise results from estimate_truncation", "topics": [ "summary.estimate_truncation" ] }, { "page": "summary.forecast_infections", "title": "Summary output from forecast_infections", "topics": [ "summary.forecast_infections" ] }, { "page": "trunc_opts", "title": "Truncation Distribution Options", "topics": [ "trunc_opts" ] }, { "page": "update_secondary_args", "title": "Update estimate_secondary default priors", "topics": [ "update_secondary_args" ] } ], "_pkglogo": "https://github.com/epiforecasts/EpiNow2/raw/HEAD/man/figures/logo.png", "_readme": "https://github.com/epiforecasts/EpiNow2/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "BH", "callr", "checkmate", "cli", "cpp11", "data.table", "desc", "distributional", "farver", "formatR", "futile.logger", "futile.options", "generics", "ggplot2", "glue", "gridExtra", "gtable", "inline", "isoband", "labeling", "lambda.r", "lifecycle", "loo", "lubridate", "magrittr", "matrixStats", "numDeriv", "otel", "patchwork", "pillar", "pkgbuild", "pkgconfig", "posterior", "primarycensored", "processx", "ps", "purrr", "QuickJSR", "R.methodsS3", "R.oo", "R.utils", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "rlang", "rstan", "rstantools", "runner", "S7", "scales", "StanHeaders", "tensorA", "tibble", "timechange", "truncnorm", "utf8", "vctrs", "viridisLite", "withr" ], "_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" } ], "_vignettes": [ { "source": "case-studies.Rmd", "filename": "case-studies.html", "title": "Case studies and use in the literature", "engine": "knitr::rmarkdown", "headings": [ "Case studies", "Public health surveillance", "Literature", "By package authors", "By others" ], "created": "2022-10-17 12:20:39", "modified": "2026-05-19 18:46:38", "commits": 8 }, { "source": "estimate_infections_options.Rmd", "filename": "estimate_infections_options.html", "title": "Examples: estimate_infections()", "engine": "knitr::rmarkdown", "headings": [ "Set up", "Data", "Parameters", "Delays: incubation period and reporting delay", "Generation time", "Initial reproduction number", "Running the model", "Default options", "Reducing the accuracy of the approximate Gaussian Process", "Adjusting for future susceptible depletion", "Adjusting for truncation of the most recent data", "Projecting the reproduction number with the Gaussian Process", "Fixed reproduction number", "Breakpoints", "Weekly random walk", "No delays", "Non-parametric infection model" ], "created": "2023-10-03 09:41:37", "modified": "2026-02-03 20:35:53", "commits": 15 }, { "source": "estimate_dist_workflow.Rmd", "filename": "estimate_dist_workflow.html", "title": "Fitting delay distributions with estimate_dist()", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Set up", "Simulating censored delay data", "Setting priors", "Fitting the model", "Checking parameter recovery" ], "created": "2026-05-19 18:48:38", "modified": "2026-05-19 19:46:33", "commits": 2 }, { "source": "forecasting_multiple_data_streams.Rmd", "filename": "forecasting_multiple_data_streams.html", "title": "Forecasting multiple data streams", "engine": "knitr::rmarkdown", "headings": [ "Background", "Setup", "Data", "Estimating infections", "Estimating secondary scaling and delay", "Forecasting secondary outcomes" ], "created": "2025-02-27 20:45:13", "modified": "2026-02-05 08:56:52", "commits": 3 }, { "source": "gaussian_process_implementation_details.Rmd", "filename": "gaussian_process_implementation_details.html", "title": "Gaussian Process implementation details", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Definition", "Matérn 3/2 covariance kernel (the default)", "Squared exponential kernel", "Ornstein-Uhlenbeck (Matérn 1/2) kernel", "Matérn 5/2 covariance kernel", "Hilbert space approximation", "Modelling the reproduction number", "References" ], "created": "2023-04-27 14:17:41", "modified": "2026-06-05 12:45:15", "commits": 10 }, { "source": "EpiNow2.Rmd", "filename": "EpiNow2.html", "title": "Getting started with EpiNow2", "engine": "knitr::rmarkdown", "headings": [ "Quick start", "Reporting delays, incubation period and generation time", "epinow()", "regional_epinow()" ], "created": "2024-01-09 18:44:03", "modified": "2026-02-25 12:42:24", "commits": 19 }, { "source": "estimate_dist.Rmd", "filename": "estimate_dist.html", "title": "Model definition: estimate_dist()", "engine": "knitr::rmarkdown", "headings": [ "Overview", "Data and notation", "Likelihood", "Continuous formulation", "Truncation", "Discrete observation likelihood", "Untruncated approximation", "Primary event distribution", "Delay families and parameterisations", "Priors", "References" ], "created": "2026-05-19 18:48:38", "modified": "2026-05-19 18:48:38", "commits": 1 }, { "source": "estimate_infections.Rmd", "filename": "estimate_infections.html", "title": "Model definition: estimate_infections()", "engine": "knitr::rmarkdown", "headings": [ "Infection model", "Renewal equation model", "Initialisation", "Infections", "Time-varying reproduction number", "Beyond the end of the observation period", "Adjusting for susceptible population depletion", "Non-Mechanistic infection model", "Delays and scaling", "Observation model", "Truncation", "References" ], "created": "2022-10-17 12:20:39", "modified": "2026-06-05 12:45:15", "commits": 17 }, { "source": "estimate_secondary.Rmd", "filename": "estimate_secondary.html", "title": "Model definition: estimate_secondary()", "engine": "knitr::rmarkdown", "headings": [], "created": "2022-10-17 12:20:39", "modified": "2025-02-03 17:05:54", "commits": 5 }, { "source": "estimate_truncation.Rmd", "filename": "estimate_truncation.html", "title": "Model definition: estimate_truncation()", "engine": "knitr::rmarkdown", "headings": [ "Model", "Priors" ], "created": "2022-10-17 12:20:39", "modified": "2026-06-05 09:20:06", "commits": 11 }, { "source": "model_features.Rmd", "filename": "model_features.html", "title": "Model features", "engine": "knitr::rmarkdown", "headings": [ "Component overview", "Estimation models", "Infection model", "Secondary model", "Truncation / nowcasting", "Delay distribution fitting", "Model configuration", "Reproduction number", "Gaussian process", "Delay distributions", "Observation model", "Options summary", "Forward simulation and forecasting", "Simulation", "Forecasting", "Supporting utilities", "Data preprocessing", "Workflow wrappers", "Stan backend" ], "created": "2026-05-07 13:44:03", "modified": "2026-05-19 18:48:38", "commits": 2 }, { "source": "model_overview.Rmd", "filename": "model_overview.html", "title": "Model overview", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Architecture", "Relationship between models", "Where to look next" ], "created": "2026-05-07 13:44:03", "modified": "2026-05-19 18:48:38", "commits": 2 }, { "source": "prior_choice_guide.Rmd", "filename": "prior_choice_guide.html", "title": "Prior choice and specification guide", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Set up", "Overview of all priors", "estimate_infections() priors", "estimate_secondary() priors", "estimate_truncation() priors", "Prior impacts and choice guidance", "Reproduction number", "Gaussian Process length scale", "Gaussian Process magnitude", "Random walk for $R_t$ (alternative to GP)", "Observation model: overdispersion", "Observation model: scaling", "For estimate_infections():", "For estimate_secondary():", "Generation time distribution", "Delays (incubation and reporting)", "Truncation", "Model choice in estimate_infections()", "Priors for estimate_secondary()", "Delay between primary and secondary", "Priors for estimate_truncation()", "Truncation distribution parameters", "Practical workflow for prior specification", "Step 1: Start with defaults", "Step 2: Identify candidates for modification", "Step 3: Modify one prior at a time", "Step 4: Check prior predictive distributions", "Step 5: Check model convergence", "Common pitfalls and recommendations", "Pitfall 1: Over-informative priors without justification", "Pitfall 2: Ignoring generation time and delays", "Pitfall 3: Estimating too many uncertain parameters", "Pitfall 4: Wrong time scale for length scale", "Pitfall 5: Forgetting the max parameter", "References and further reading", "Key papers" ], "created": "2025-11-13 14:01:42", "modified": "2026-03-12 08:09:40", "commits": 6 }, { "source": "delays.Rmd", "filename": "delays.html", "title": "Understanding delay distributions in EpiNow2", "author": "EpiNow2 Team", "engine": "knitr::rmarkdown", "headings": [ "What delay distributions represent", "Specifying delays", "Why naive discretisation is biased", "How primarycensored corrects this", "Composing multiple delays", "Truncation", "Fitting delay distributions from data", "References" ], "created": "2026-05-07 13:44:03", "modified": "2026-05-19 18:48:38", "commits": 2 }, { "source": "epinow.Rmd", "filename": "epinow.html", "title": "Using epinow() for running in production mode", "engine": "knitr::rmarkdown", "headings": [ "Running the model on a single region", "Running the model simultaneously on multiple regions" ], "created": "2023-10-03 09:41:37", "modified": "2026-02-03 21:25:06", "commits": 17 }, { "source": "estimate_infections_workflow.Rmd", "filename": "estimate_infections_workflow.html", "title": "Workflow for Rt estimation and forecasting", "engine": "knitr::rmarkdown", "headings": [ "Data", "Set up", "Parameters", "Delay distributions", "Generation intervals", "Reporting delays", "Truncation", "Completeness of reporting", "Initial reproduction number", "Weighing delay priors", "Estimation and forecasting", "Forecasting secondary outcomes", "Interpretation", "Evaluating forecasts with scoringutils" ], "created": "2023-10-03 09:41:37", "modified": "2026-05-07 10:44:14", "commits": 17 } ], "_score": 12.36156626956929, "_indexed": true, "_nocasepkg": "epinow2", "_universes": [ "epiforecasts", "sbfnk" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.8.0.9000", "date": "2026-06-05T20:09:22.000Z", "distro": "noble", "arch": "aarch64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "303199bfc7aa26f00555e5206880cf5a4550cc1cded5b96d5198c0f2969974ca", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" }, { "r": "4.7.0", "os": "linux", "version": "1.8.0.9000", "date": "2026-06-05T20:09:19.000Z", "distro": "noble", "arch": "x86_64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "c8c40a707045729ee1dab256b99623bc1a754ce9f0ccd79b7dcba7fa667653b3", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" }, { "r": "4.6.0", "os": "linux", "version": "1.8.0.9000", "date": "2026-06-05T20:09:34.000Z", "distro": "noble", "arch": "aarch64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "2e064aebea08f56e4f45f5d964f9a56dc42a531ef091fe39de58080e75bd44c7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" }, { "r": "4.6.0", "os": "linux", "version": "1.8.0.9000", "date": "2026-06-05T20:09:33.000Z", "distro": "noble", "arch": "x86_64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "d3bc1199c065ce747959e2ce204cc54a9c758f92cfac3656a0df3d38aad4930d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" }, { "r": "4.5.3", "os": "mac", "version": "1.8.0.9000", "date": "2026-06-05T20:09:12.000Z", "arch": "aarch64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "d024518a54528e171d5b032396b9d3d8004f690d23d40cb54f3b2fca131577ac", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" }, { "r": "4.5.3", "os": "mac", "version": "1.8.0.9000", "date": "2026-06-05T20:11:46.000Z", "arch": "x86_64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "503a09bab6c70cf41ae87f396b348bb75531aefc36561fc8e0266a2198646c33", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" }, { "r": "4.6.0", "os": "mac", "version": "1.8.0.9000", "date": "2026-06-05T20:10:05.000Z", "arch": "aarch64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "979e80bad84e972f6acc97ea7642ee6a42c5fa1bf02caeb177d4be5709e52218", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" }, { "r": "4.6.0", "os": "mac", "version": "1.8.0.9000", "date": "2026-06-05T20:16:44.000Z", "arch": "x86_64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "38f84f1a4fcb7c44e96548fb8e9f72ca6de02b2a34996d664ca3ca69559c5c07", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" }, { "r": "4.7.0", "os": "win", "version": "1.8.0.9000", "date": "2026-06-05T20:08:35.000Z", "arch": "x86_64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "95df586fdef5d9e828f317b1414471a5777a6f81e20a89f7837191add8bfb23d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" }, { "r": "4.5.3", "os": "win", "version": "1.8.0.9000", "date": "2026-06-05T20:08:56.000Z", "arch": "x86_64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "44f8d9af0637106a027d5113d85c80977106ffe2c48f3484483634b6164a3ff2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" }, { "r": "4.6.0", "os": "win", "version": "1.8.0.9000", "date": "2026-06-05T20:08:51.000Z", "arch": "x86_64", "commit": "b405f7061811a5b982d2bca638488344de3139d6", "fileid": "1b42152583c2aacaef6f887652a069f822f6e0b69b63528c3b6e612043c9f15d", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/epiforecasts/actions/runs/27036593271" } ] }