MaximeMaW/MeningitisDynamics

Analysis scripts for the paper "Characterization and detection of bacterial meningitis localized epidemics in the African meningitis belt using high spatial resolution surveillance data" Supporting analyses for the paper "Characterization and detection of bacterial meningitis localized epidemics in the African meningitis belt using high spatial resolution surveillance data" ============== Here are the scripts used to derive the figures of the paper "Characterization and detection of bacterial meningitis localized epidemics in the African meningitis belt using high spatial resolution surveillance data" (manuscript in preparation). The aim is to make sure that the analyses are fully reproducible, that is: - The full dataset will be available upon request. They remain the property of the Direction de la Lutte contre la Maladie, Burkina Faso - The preprocessing and analysis scripts are made public here This document is organized as follows: 1. Organization of the repository: where to find the analyses, the scripts, etc. 2. Processed data: we introduce the intermediate analysis files that were derived and then used for the analysis 3. Figures: we introduce the rationale and the key steps of the analysis behind each figure (this do not prevent you from reading the code) 4. Additional analyses: additional analysis that might be of interest, even if they didn't end up in the paper. These scripts are released under the GNU General Public License v3 or newer (GPLv3+). This means that you have the right to use, to study and modify the code and to share the modifications. Please keep a mention of the initial author. Also, the scripts are written in `R`. Sometimes the code might be hard to read/hard to follow, feel free to contact the authors for clarification. ## Organization of the repository ### File architecture *Disclaimer:* this repository do not contain the datasets. These datasets are available upon request at the DLM or from the corresponding author. The repository is organized in several folders and subfolders: 1. `scripts`: this folder contains only the scripts to generate the data. These are the same scripts as the ones presented in this …