Filtered (real-time/causal) and smoothed (retrospective) estimation of the time-varying effective reproduction number (Rt) from case-count time series, using the EpiFilter algorithm of Parag (2021) <doi:10.1371/journal.pcbi.1009347>, together with a one-step-ahead in-sample prediction check, a genuine out-of-sample one-step forecast with predictive intervals, elimination probability P(Rt < 1), and forecast calibration metrics (mean absolute error, mean squared error, root mean squared error, empirical coverage, and the weighted interval score of Bracher et al. (2021) <doi:10.1371/journal.pcbi.1008618>). Disease-agnostic: works for any pathogen given a known generation interval.
| Version: | 0.1.1 |
| Depends: | R (≥ 3.5) |
| Imports: | graphics, grDevices, stats, utils |
| Suggests: | testthat (≥ 3.0.0), knitr, rmarkdown |
| Published: | 2026-08-21 |
| DOI: | 10.32614/CRAN.package.RtForecastR |
| Author: | Raj Subedi [aut, cre, cph] (Copyright holder for all files except epiFilter.R, epiSmoother.R, and the original recursPredict.R logic (see Kris V. Parag entry); author of R/recursPredict.R's configurable-grid maxI extension and R/recursPredictQuantiles.R), Kris V. Parag [ctb, cph] (Author/copyright holder of the original EpiFilter algorithm (epiFilter, epiSmoother, recursPredict); files R/epiFilter.R, R/epiSmoother.R and R/recursPredict.R are unmodified or lightly modified ports of that work, released under GPL-3) |
| Maintainer: | Raj Subedi <rajsubediresearch at gmail.com> |
| BugReports: | https://github.com/rajsubediresearch/RtForecastR/issues |
| License: | GPL-3 |
| URL: | https://github.com/rajsubediresearch/RtForecastR |
| NeedsCompilation: | no |
| Language: | en-US |
| Materials: | NEWS |
| CRAN checks: | RtForecastR results |
| Reference manual: | RtForecastR.html , RtForecastR.pdf |
| Vignettes: |
RtForecastR walkthrough (source, R code) |
| Package source: | RtForecastR_0.1.1.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: RtForecastR_0.1.1.zip |
| macOS binaries: | r-release (arm64): RtForecastR_0.1.1.tgz, r-oldrel (arm64): RtForecastR_0.1.1.tgz, r-release (x86_64): RtForecastR_0.1.1.tgz, r-oldrel (x86_64): RtForecastR_0.1.1.tgz |
| Old sources: | RtForecastR archive |
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