Reproductive Number

Software

WhiteLabRt

We have recently created a new R package (WhiteLabRt) that improves performance on the methods proposed in Zhou et al and Li et al. This is loaded on to CRAN and uses C and Stan to improve computation time.

These functions perform the following tasks:

• Estimate spatially localized reproductive numbers that can incorporate mobility data.
• Account for reporting delays in data and nowcast cases to get more up to date estimates.

Estimation of Local reproductive numbers

This method is described in Li et al and allows one to estimate \(R_t\) accounting for imported cases from other regions. Code for implementing the method is found here.

Helpful tools

We are working on a bookdown to describe all available \(R_t\) estimation methods with implementation in R to be useful for practitioners. This is a work in progress here.

Publications

• Zhou Z, Thompson RN, Kolaczyk ED, White LF. Estimation of heterogeneous instantaneous reproduction numbers with application to characterize SARS-CoV-2 transmission in Massachusetts counties. PLoS Comput Biol. 2022 Sep;18(9):e1010434. link
• Li T, White LF. Bayesian back-calculation and nowcasting for line list data during the COVID-19 pandemic. 2021 Plos Comp Biol, 2021 Jul 12;17(7):e1009210. link
• Li W, Bulekova K, Gregor B, White LF, Kolaczyk ED. Estimation of local time-varying reproduction numbers in noisy surveillance data. Philos Trans A Math Phys Eng Sci. 2022 Oct 3;380(2233):20210303. doi: 10.1098/rsta.2021.0303. link