amuxlhanga/mozambique-malaria-patterns-2017-2023

Reproducible analysis code for the district-level analysis of spatial and seasonal malaria transmission heterogeneity in Mozambique, 2017–2023. # Chapter 1 manuscript results pipeline ## Quick start for the complete package The complete package already includes the required local input files in `data_raw/`. Open `Chapter1_manuscript_results.Rproj`, then run: ```r source("install_packages.R") # only once source("check_inputs.R") source("run_all.R") ``` Do not set `CH1_DATA_DIR` unless you intentionally want to use another data folder. The selected folder is printed at the start of the run. This project contains only the code needed to reproduce the results, two tables and fourteen figures reported in the manuscript **“Exploring malaria patterns in Mozambique: a subnational data-driven analysis of spatial and seasonal transmission heterogeneity (2017–2023)”**. ## 1. Data placement The restricted NMCP source data are not included. Point the project to the existing data directory before execution: ```r Sys.setenv(CH1_DATA_DIR = "C:/path/to/data") ``` ## 2. Install packages From the project root: ```r source("install_packages.R") ``` The geospatial packages may require system libraries supported by the local R installation. ## 3. Run everything ```r source("run_all.R") ``` or from a terminal: ```bash Rscript run_all.R ``` The pipeline writes: - manuscript figures as 600-dpi PNG and TIFF files to `outputs/figures/`; - Tables 1 and 2 to `outputs/tables/`; ## Analytical scope The pipeline deliberately excludes analyses that do not appear in the manuscript. It uses district-month data for 2017–2023, RDT-confirmed cases for the descriptive incidence results, annual WHO transmission strata, wavelet coherence, environmental NB2 models, vector composition, categorical insecticide resistance, intervention coverage and top-20% hotspot persistence. The script `scripts/18_manuscript_numeric_results.R` compares key recalculated values with those reported in the manuscript so discrepancies are visible rather than silently overwritten.