Projected long-term effects of colorectal cancer screening disruptions following the COVID-19 pandemic
This repository contains code for the paper Nascimento de Lima et al, Projected long-term effects of colorectal cancer screening disruptions following the COVID-19 pandemic, eLife https://doi.org/10.7554/eLife.85264
All figures and tables from our analysis can be reproduced from summary output files using publicly available data and free software. The models underlying the analysis (CRC-SPIN and MISCAN) are not made publicly available per current CISNET policy.
We used R version 4.2.1 (2022-06-23) and RStudio 2022.07.1 to perform this analysis. Using an up-to-date R installation (i.e., R> 4.0.0), run the 00_install_dependencies.R script to install all dependencies. Alternatively, open the unequal-recovery.covid-19.Rproj file with RStudio and use renv::restore() to use the same package versions we used.
Open the unequal-recovery.covid-19.Rproj project with RStudio and run the 01_tables_plots.R script to generate the figures and tables included in our manuscript. Outputs will be created in the ./output folder.
- ./R/funs: contains the functions and classes used in the analysis.
- ./input: contains all analysis inputs. Includes data generated by CISNET models. Note that the models and code that produce those inputs are not released in this repository.
- ./output: houses intermediate outputs created by the scripts.
Reach out to Pedro Nascimento de Lima for questions related to this repository.
This repository is released as open-source software under a GPL-2.0 license. See the LICENSE.md file. Copyright (c) 2022 by paper authors: Pedro Nascimento de Lima, Rosita van den Puttelaar, Anne I. Hahn, Matthias Harlass, Nicholson Collier, Jonathan Ozik, Ann G. Zauber, Iris Lansdorp-Vogelaar, Carolyn M. Rutter.