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rtestim  

Estimate the Effective Reproductive Number with Trend Filtering
View on CRAN: Click here


Download and install rtestim package within the R console
Install from CRAN:
install.packages("rtestim")

Install from Github:
library("remotes")
install_github("cran/rtestim")

Install by package version:
library("remotes")
install_version("rtestim", "1.0.1")



Attach the package and use:
library("rtestim")
Maintained by
Daniel J. McDonald
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2025-07-05
Latest Update: 2025-07-05
Description:
Use trend filtering, a type of regularized nonparametric regression, to estimate the instantaneous reproduction number, also called Rt. This value roughly says how many new infections will result from each new infection today.Values larger than 1 indicate that an epidemic is growing while those less than 1 indicate decline. For more details about this methodology, see Liu, Cai, Gustafson, and McDonald (2024) <doi:10.1371/journal.pcbi.1012324>.
How to cite:
Daniel J. McDonald (2025). rtestim: Estimate the Effective Reproductive Number with Trend Filtering. R package version 1.0.1, https://cran.r-project.org/web/packages/rtestim. Accessed 05 Jun. 2026.
Previous versions and publish date:
1.0.0 (2025-07-05 20:50), 1.0.1 (2025-10-24 20:50)
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Complete documentation for rtestim
Functions, R codes and Examples using the rtestim R package
Full rtestim package functions and examples
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