This repository provides materials for an article, "A renewal-equation approach to estimating $R_t$ and infectious disease case counts in the presence of reporting delays" by Sumali Bajaj, Robin Thompson and Ben Lambert.

We use renv R package to manage the environment, and after cloning this article and opening the R project file, the R environment can be reproduced by running the following from the RStudio console:

renv::restore()

We use the targets R package to create reproducible data analysis pipelines. To rerun all analyses, type the following in the Rstudio console:

targets::tar_make()

To generate only a specific target, first consult the _targets.R file to find a particular target name; this name will then be used as an argument to tar_make(). We illustrate this for the file_plot_projections_waning_over_png target which generates the projections_waning.png file:

targets::tar_make(file_plot_projections_waning_over_png)