{ "_id": "6ad1efc129625c14e47af1df", "Package": "diseasenowcasting", "Title": "Nowcast Time Series of Epidemiological Cases", "Version": "2.4.0", "Authors@R": "c(person(\"Rodrigo\", \"Zepeda-Tello\", role = c(\"aut\", \"cre\"),\nemail = \"rzepeda17@gmail.com\",\ncomment = c(ORCID = \"0000-0003-4471-5270\")),\nperson(\"Rami\", \"Yaari\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-8808-8937\")),\nperson(\"Matteo\", \"Perini\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-9465-6216\")),\nperson(\"Tal\", \"Robin\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-3128-2499\")),\nperson(\"Teresa\", \"Yamana\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0001-8349-3151\")),\nperson(\"Jeffrey\", \"Shaman\", role = \"ctb\"),\nperson(given = \"Columbia University in the City of New York\",\nrole = c(\"cph\", \"fnd\")))", "Description": "Implements Bayesian nowcasting models for incident disease\ncases using a censored point-process approach. The reporting\ndelay is modelled directly as a stochastic process, jointly\nwith the epidemic dynamics, via a censored likelihood.\nInference uses RTMB (CppAD autodiff + Laplace approximation).\nSupports arbitrary epidemic models (including HSGP, AR1, SIR),\narbitrary delay families (including LogNormal, GenGamma,\nDirichlet), stratified data, extreme-delay detection, and\nbacktesting.", "License": "MIT + file LICENSE", "URL": "https://rodrigozepeda.github.io/diseasenowcasting/,\nhttps://github.com/RodrigoZepeda/diseasenowcasting", "BugReports": "https://github.com/RodrigoZepeda/diseasenowcasting/issues", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Additional_repositories": "https://kaskr.r-universe.dev,\nhttps://davisvaughan.r-universe.dev,\nhttps://rodrigozepeda.r-universe.dev", "VignetteBuilder": "knitr", "Config/testthat/edition": "3", "LazyData": "true", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://rodrigozepeda.r-universe.dev", "Date/Publication": "2026-09-09 18:55:43 UTC", "RemoteUrl": "https://github.com/rodrigozepeda/diseasenowcasting", "RemoteRef": "HEAD", "RemoteSha": "d90a3e36af7340c056f83e461c6147eb304077d5", "NeedsCompilation": "no", "Packaged": { "Date": "2026-10-16 08:53:25 UTC", "User": "root" }, "Author": "Rodrigo Zepeda-Tello [aut, cre] (ORCID:\n),\nRami Yaari [aut] (ORCID: ),\nMatteo Perini [aut] (ORCID: ),\nTal Robin [ctb] (ORCID: ),\nTeresa Yamana [ctb] (ORCID: ),\nJeffrey Shaman [ctb],\nColumbia University in the City of New York [cph, fnd]", "Maintainer": "Rodrigo Zepeda-Tello ", "_user": "rodrigozepeda", "_type": "src", "_file": "diseasenowcasting_2.4.0.tar.gz", "_fileid": "https://r2.ropensci.org/3b849a52008fe5c0a8989d8b2c4c0434e38df944838044a9ff8698c113c67032", "_filesize": 4387535, "_sha256": "3b849a52008fe5c0a8989d8b2c4c0434e38df944838044a9ff8698c113c67032", "_expires": "2027-01-24T09:34:55.000Z", "_created": "2026-10-16T08:53:25.000Z", "_published": "2026-10-16T09:34:57.617Z", "_buildurl": "https://github.com/r-universe/rodrigozepeda/actions/runs/38876104759", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 116893552028, "time": 269, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12036340000" }, { "job": 116893551948, "time": 353, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12035488997" }, { "job": 116893551963, "time": 279, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12037093255" }, { "job": 116893552007, "time": 198, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12037059141" }, { "job": 116891603846, "time": 319, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12035946509" }, { "job": 116893552046, "time": 185, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12036026445" }, { "job": 116893552009, "time": 306, "config": "windows-devel-x86_64", 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Advanced: A differential equations epidemic process" ], "created": "2026-06-16 21:19:07", "modified": "2026-06-22 20:37:04", "commits": 5 }, { "source": "introduction.Rmd", "filename": "introduction.html", "title": "Introduction to diseasenowcasting: Real-Time Epidemic Nowcasting", "author": "diseasenowcasting team", "engine": "knitr::rmarkdown", "headings": [ "Native modelling and the shared workflow", "Your data: the tbl_now format", "Example 1 -- Dengue fever (setting up a stratified nowcast)", "Example 2 -- Mpox (modifying the nowcast model)", "Example 3 -- Comparing models with a backtest", "When a report is not yet a case: the revision process", "Example 4 -- Letting the package choose the model (auto_nowcast())", "Updating the chosen model as new data arrive", "Example 5 -- Count-cumulative revisions and a historical origin", "Saving and loading a fitted nowcast", "Combining diseasenowcasting models in an ensemble", "Next steps" ], "created": "2026-06-01 20:58:04", "modified": "2026-09-09 11:24:59", "commits": 18 }, { "source": "Nowcasting_at_the_start_of_an_Epidemic.Rmd", "filename": "Nowcasting_at_the_start_of_an_Epidemic.html", "title": "Nowcasting at the Start of an Epidemic", "author": "diseasenowcasting team", "engine": "knitr::rmarkdown", "headings": [ "TL;DR", "The challenge: few data points", "0) Prelude: Data preparation", "1) Prior choices at the start of an epidemic", "1.1 The SIR model: mechanistic priors", "1.2 The AR(1) model: trend priors", "1.3 The HSGP model: kernel priors", "2) Experiments with the prior: prior-predictive simulation", "2.1) SIR -- moving R0.", "2) COVID-19 Colombia: example from 1 day to 3 months", "2.2 Fitting each model across the four windows", "2.3 Comparing the three models across windows", "2.4 A rule of thumb", "3) Conclusion: When to fit what?" ], "created": "2026-06-03 05:06:54", "modified": "2026-09-09 11:24:59", "commits": 7 }, { "source": "Understanding_Priors.Rmd", "filename": "Understanding_Priors.html", "title": "Understanding Priors and Hyperparameters in diseasenowcasting", "author": "diseasenowcasting team", "engine": "knitr::rmarkdown", "headings": [ "Quick reference", "What the rest of the vignette shows:", "1. Likelihood prior: NB precision (phi)", "2. Reporting-delay parameters", "2.1 Log-Normal delay", "2.1.1 Location (mu)", "2.1.2 Scale (sigma)", "2.2 Generalized-Gamma delay", "2.2.1 Location (mu)", "2.2.2 Scale (sigma)", "2.2.3 Tail shape (Q)", "2.3 Dirichlet (non-parametric) delay", "2.3.1 Concentration (alpha)", "3. Epidemic-process parameters", "3.1 HSGP", "3.1.1 Amplitude (alpha)", "3.1.2 Length-scale (ell)", "3.1.4 HSGP: number of basis functions (num_basis)", "3.2 AR(1)", "3.2.1 Autocorrelation (phi)", "3.2.2 Innovation SD (sigma)", "3.3 SIR", "3.3.1 Basic reproduction number (R0)", "3.3.2 Recovery rate (gamma)", "3.3.3 Susceptible fraction (N_eff)", "3.3.4 Total population (N_pop)", "4. Covariate priors (covariate_prior)", "5. Practical guide" ], "created": "2026-06-04 20:35:21", "modified": "2026-06-16 21:19:07", "commits": 5 } ], "_score": 5.261024833992398, "_indexed": true, "_nocasepkg": "diseasenowcasting", "_universes": [ "rodrigozepeda" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.4.0", "date": "2026-10-16T08:56:00.000Z", "distro": "resolute", "commit": "d90a3e36af7340c056f83e461c6147eb304077d5", "fileid": "https://r2.ropensci.org/ac104aa9db8df8dd24ccbec4079bd614838a9f90e3d20af4919ca3e6fa4b76fd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rodrigozepeda/actions/runs/38876104759" }, { "r": "4.6.1", "os": "linux", "version": "2.4.0", "date": "2026-10-16T08:56:10.000Z", "distro": "resolute", "commit": "d90a3e36af7340c056f83e461c6147eb304077d5", "fileid": "https://r2.ropensci.org/55f45aafc065817f18813c3df809b272952c2651fd0331eb00dd018c8445ad8f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rodrigozepeda/actions/runs/38876104759" }, { "r": "4.5.3", "os": "mac", "version": "2.4.0", "date": "2026-10-16T09:31:11.000Z", "commit": "d90a3e36af7340c056f83e461c6147eb304077d5", "fileid": "https://r2.ropensci.org/b5e1e41c7b0ee25701bf9fbfa8d9921d646e64fca4f825d7c6dcd1d71790bc14", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rodrigozepeda/actions/runs/38876104759" }, { "r": "4.6.1", "os": "mac", "version": "2.4.0", "date": "2026-10-16T09:29:21.000Z", "commit": "d90a3e36af7340c056f83e461c6147eb304077d5", "fileid": "https://r2.ropensci.org/a9b0c05c80f6034b9771fa9d01b9b97137d2caa028664e58ed8e77f9524422ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rodrigozepeda/actions/runs/38876104759" }, { "r": "4.6.0", "os": "wasm", "version": "2.4.0", "date": "2026-10-16T08:56:52.000Z", "commit": "d90a3e36af7340c056f83e461c6147eb304077d5", "fileid": "https://r2.ropensci.org/a312c3795a1fc7657ac1ec0e30d7c2f995d07cd6e8f076a0d9df47bf60d74b53", "status": "success", "buildurl": "https://github.com/r-universe/rodrigozepeda/actions/runs/38876104759" }, { "r": "4.7.0", "os": "win", "version": "2.4.0", "date": "2026-10-16T08:54:50.000Z", "commit": "d90a3e36af7340c056f83e461c6147eb304077d5", "fileid": "https://r2.ropensci.org/4d6af185821506815d33acd4c43626c4a573aa99bd0257d2ee115815c5a10fe8", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rodrigozepeda/actions/runs/38876104759" }, { "r": "4.5.3", "os": "win", "version": "2.4.0", "date": "2026-10-16T08:55:22.000Z", "commit": "d90a3e36af7340c056f83e461c6147eb304077d5", "fileid": "https://r2.ropensci.org/a58e2bbf8ce0c0322d9d3de5366d63a8048d4d83aa96da09c02159ed4b5a9754", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rodrigozepeda/actions/runs/38876104759" }, { "r": "4.6.1", "os": "win", "version": "2.4.0", "date": "2026-10-16T08:55:22.000Z", "commit": "d90a3e36af7340c056f83e461c6147eb304077d5", "fileid": "https://r2.ropensci.org/f8119d3a2ef62fbd17d12297ae4cbfbe4ad1a4184c2e075878c9dc6da278659c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/rodrigozepeda/actions/runs/38876104759" } ] }