covasim/covid_es

Code for paper "Cost-effectiveness of wastewater-based environmental surveillance for SARS-CoV-2 in Blantyre, Malawi and Kathmandu, Nepal: a model-based study" # Cost-effectiveness of wastewater-based environmental surveillance for SARS-CoV-2 in Blantyre, Malawi and Kathmandu, Nepal: a model-based study This code is released in support of the following manuscript: > Mvundura M, Ngwira LG, Shrestha KB, Tuladhar R, Gauld J, Kerr C, Barnes K, Anscombe C, Sharma B, Feasey N. Cost-effectiveness of wastewater-based environmental surveillance for SARS-CoV-2 in Blantyre, Malawi and Kathmandu, Nepal: A model-based study. *PLOS Glob Public Health*. 2025 Apr 24;5(4):e0004439. doi: 10.0.5.91. PMID: 40273116; PMCID: PMC12021199. ## Structure All code used to generate model-based results is in this repository. The structure is as follows: - The Python library code is in `covasim_es`. - Script files used to run and process the simulations for Malawi are in `malawi_scripts`. The main file used to generate the results is `sweep_lines.py`, but other scripts are included for completeness. These scripts are computationally intensive, requiring roughly 140 core-hours on a high-performance compute cluster. Do not try to run on your laptop without first setting `debug = True`. - Equivalent scripts for Nepal are in `nepal_scripts`. - Scripts used to produce the figures in the manuscript are in `figures`. - The pre-generated data files loaded by the scripts are stored in `results`. These are in compressed binary format, but can be loaded as pandas dataframes (and then exported to Excel if desired) using Sciris (specifically, `sc.load()`). ## Installation 1. Ensure you have Python installed (if you haven't installed Python already, the easiest is to use Anaconda; an out-of-the-box system Python installation is unlikely to work). 2. In a terminal (or Windows command prompt), type `pip install -e .` to install (note the "`.`" at the end of the command, this is critical!). 3. To test your installation, `import covasim_es` should work from a Python prompt. If you're using R, you need to have R installed. You also ne …