Practical considerations for detectingchanges in the effective reproductive number, Rt.
Code by Katie Gostic, Ed Baskerville and Lauren McGough.
Last updated 18-June-2020.
Click the above link to read the latest version of the manuscript. Contact kgostic@uchicago.edu with comments.
We will post the medRxiv doi once it becomes available.
This directory contains functions and wrappers used to perform analyses:
simulation.R
- code to generate synthetic data using an SIR or SEIR-type model, deterministic or stochastic.funs_simulation-sweep.R
- wrapper functions for epidemic simulation.infer_times_of_infection_observation.R
- functions to infer times of observation from SEIR times of infection, and to infer times of infection from times of observation by (1) drawing samples from a known delay distribution, or (2) shifting back in time by the mean delay to observation.rtlive.R
andrtlive.stan
together provide code to reporduce an adaptation of the Bettencourt & Ribeiro method for Rt estimation popularized by rt.live.util.R
- various utility functions, including wrappers to estimate Rt using the methods of Cori et al., Wallinga & Teunis, and using methods adapted from Bettencourt & Ribeiro by rt.live. The first two methods are implemented in the package EpiEstim. The final method uses the rstan implementation above.caseR.R
- Functions to calculate the exact case reproductive number within the synthetic data (dahsed black lines shown in Fig. 2 and Fig. B.2).Rc_math.Rmd
- Notes on the math used to calculate the case reproductive number exactly.
This directory contains scripts and notebooks used to run analyses and generate figures:
01-simulate_data.R
- Specify inputs, generate synthetic data and save to a directory calledR0-xx/
.02-Analyze_synthetic_data.Rmd
- Annotated code performs the analyses and makes all plots shown in Fig. 2, 5 and 6, and appendix Fig. B.3.02-make_Fig_2_appendix.Rmd
- Code performs analyses and generates Fig. B2, an alternate version of Fig. 2 in the main text, which compares the performance of Cori, Wallinga and Teunis, and Bettencourt and Ribeiro when the time series is truncated as Rt rises or falls.03-Make_Fig_4.Rmd
- Annotated code performs the analyses and makes all plots shown in Fig. 4.04-Make_Fig_deconvolution.Rmd
- Annotated code performs the analyses and makes the plot shown in the appendix, a tutorial on why deconvolution methods are needed.