Penn State - Center for Infectious Disease Dynamics (CIDD) - Boni Lab
This repository contains a frozen snapshot of the code and intermediate data used to prepare the manuscript by Zupko et al. (2022) which appeared in PLOS Global Public Helath. Due to the size of the intermediate data (207 MB) this repository uses Git Large File Storage and may be limited in terms of bandwidth as a result. All studies run by the simulation use YAML files (in Studies) to provide the configuration and ASC files (in Data/GIS) for spatial data.
Due to the complex nature of the simuation, primary living documentation to build and run the simuation is hosted with the repository that contains active development. The version 4.1.0 code base was used to run the replicates used in manuscript revisions, while the earlier 4.0.0 code base was used for th orginal draft submitted to medRxiv.
Please cite the manuscript as follows:
Zupko, R. J., Nguyen, T. D., Somé, A. F., Tran, T. N.-A., Gerardin, J., Dudas, P., Giang, D. D. H., Tran, K. T., Wesolowski, A., Ouédraogo, J.-B., & Boni, M. F. (2022). Long-term effects of increased adoption of artemisinin combination therapies in Burkina Faso. PLOS Global Public Health, 2(2), e0000111. https://doi.org/10.1371/journal.pgph.0000111
Contents of the Study directory are organized in the following fashion:
| Type | Study Name | Filename |
|---|---|---|
| Baseline | Baseline, normal mutation rate | Baseline/bfa-fast-no-asaq.yml |
| Baseline, sensitivity | Baseline, slow mutation rate | Baseline/bfa-slow-no-asaq.yml |
| Drug Policy | Rapid Private Market Elimination | Drug Policies/bfa-rapid.yml |
| Drug Policy | Rapid Private Market Elimination, Rapid AL/DHA-PPQ MFT | Drug Policies/bfa-aldp-rapid.yml |
| Drug Policy | Rapid Private Market Elimination, Ten Year AL/DHA-PPQ MFT Phase-in | Drug Policies/bfa-aldp10-rapid.yml |
| Drug Policy | Ten Year Private Market Elimination | Drug Policies/bfa-tenyear.yml |
| Drug Policy | Ten Year Private Market Elimination, Rapid AL/DHA-PPQ MFT | Drug Policies/bfa-aldp-tenyear.yml |
| Drug Policy | Ten Year Private Market Elimination, Ten Year AL/DHA-PPQ MFT Phase-in | Drug Policies/bfa-aldp10-tenyear.yml |
| Drug Policy | Rapid AL/DHA-PPQ MFT | Drug Policies/bfa-aldp.yml |
| Drug Policy | Ten Year AL/DHA-PPQ MFT Phase-in | Drug Policies/bfa-aldp10.yml |
| Drug Policy | Rapid Private Market Elimination, Rapid 60% AL/40% DHA-PPQ MFT | Drug Policies/bfa-60-al-40-dp.yml |
| Drug Policy | Rapid Private Market Elimination, Rapid 60% AL/40% DHA-PPQ MFT | Drug Policies/bfa-70-al-30-dp.yml |
| Drug Policy | Rapid Private Market Elimination, Rapid 60% AL/40% DHA-PPQ MFT | Drug Policies/bfa-80-al-20-dp.yml |
| Drug Policy | Rapid Private Market Elimination, Rapid 60% AL/40% DHA-PPQ MFT | Drug Policies/bfa-90-al-10-dp.yml |
| Drug Policy | Rapid Private Market Elimination, AL Only First-line Therapy | Drug Policies/bfa-90-al-10-dp.yml |
| Mutation Rate | Baseline, 10x faster mutation rate | bfa-0.01983.yml |
| Mutation Rate | Baseline, 5x faster mutation rate | bfa-0.009915.yml |
| Mutation Rate | Baseline, 5x slower mutation rate | bfa-0.0003966.yml |
| Mutation Rate | Baseline, 10x slower mutation rate | bfa-0.0001983.yml |
| Mutation Rate | Rapid AL/DHA-PPQ MF, 10x faster mutation rate | bfa-aldp-0.01983.yml |
| Mutation Rate | Rapid AL/DHA-PPQ MF, 5x faster mutation rate | bfa-aldp-0.009915.yml |
| Mutation Rate | Rapid AL/DHA-PPQ MF, 5x slower mutation rate | bfa-aldp-0.0003966.yml |
| Mutation Rate | Rapid AL/DHA-PPQ MF, 10x slower mutation rate | bfa-aldp-0.0001983.yml |
| Mutation Rate | Rapid Private Market Elimination, 10x faster mutation rate | bfa-rapid-0.01983.yml |
| Mutation Rate | Rapid Private Market Elimination, 5x faster mutation rate | bfa-rapid-0.009915.yml |
| Mutation Rate | Rapid Private Market Elimination, 5x slower mutation rate | bfa-rapid-0.0003966.yml |
| Mutation Rate | Rapid Private Market Elimination, 10x slower mutation rate | bfa-rapid-0.0001983.yml |
The compiled version of the simulation used for the studies is provided in the Binaries directory, which was compiled and ran on in the following environment:
LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distributor ID: RedHatEnterpriseServer
Description: Red Hat Enterprise Linux Server release 7.9 (Maipo)
Release: 7.9
Codename: Maipo
- Malaria Simulation, version 4.1.0: https://github.com/rjzupkoii/PSU-CIDD-Malaria-Simulation
- Burkina Faso analysis and plots: https://github.com/rjzupkoii/PSU-CIDD-Burkina-Faso
- Support scripts and infrastructure: https://github.com/bonilab/PSU-CIDD-MaSim-Support
Adam Auton (2021). Red Blue Colormap (https://www.mathworks.com/matlabcentral/fileexchange/25536-red-blue-colormap), MATLAB Central File Exchange. Retrieved August 9, 2021.