bonilab/malariaibm-spatial-Rwanda-561H

Complete source code and intermediary files to accompany the manuscript published in Nature Medicine. # malariaibm-spatial-Rwanda-561H Penn State - Center for Infectious Disease Dynamics (CIDD) - Boni Lab --- # Overview This repository contains a frozen snapshot of the source code and intermediary files to accompany the manuscript by Zupko et al. (2023) which appeared in *Nature Medicine*. Due to the size of the intermediary data (479 MB, compressed) 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 simulation, primary living documentation to build and run the simulation is hosted with the repository that contains active development. The version 4.1.4 code base was used to run all replicates for the studies presented in the manuscript. --- Please cite the manuscript as follows: Zupko, R. J., Nguyen, T. D., Ngabonziza, J. C. S., Kabera, M., Li, H., Tran, T. N.-A., Tran, K. T., Uwimana, A., & Boni, M. F. (2023). Modeling policy interventions for slowing the spread of artemisinin-resistant pfkelch R561H mutations in Rwanda. *Nature Medicine*, 29, 2775-2784. Modeling policy interventio… ## Organization Contents of the `Study` directory are organized in the following fashion for the primary studies of the manuscript under the `Policy Interventions` sub-directory: | Type | Study Name | Filename | | --- | --- | --- | | AL Replacement | AL replacement with ASAQ | AL Replacement/rwa-replacement-asaq.yml | | AL Replacement | AL replacement with DHA-PPQ | AL Replacement/rwa-replacement-dhappq.yml | | Artesunate Extension | Extension of artesunate, four day course | Artesunate Extension/rwa-ae-al-4.yml | | Artesunate Extension | Extension of artesunate, five day course| Artesunate Extension/rwa-ae-al-5.yml | | Artesunate Extension | Extension of artesunate, three-day course on days 0, 1, 2; followed by second course on days 7, 8, 9 | Art …