RtForecastR: Real-Time Effective Reproduction Number Estimation and Forecasting

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

Documentation:

Reference manual:	RtForecastR.html , RtForecastR.pdf
Vignettes:	RtForecastR walkthrough (source, R code)

Downloads:

Package source:	RtForecastR_0.1.1.tar.gz
Windows binaries:	r-devel: RtForecastR_0.1.1.zip, r-release: RtForecastR_0.1.1.zip, 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

Linking:

Please use the canonical form https://CRAN.R-project.org/package=RtForecastR to link to this page.