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This repository contains code for Carlson, Carleton, Odoulami, and Trisos (2022), "The historical fingerprint and future impact of climate change on childhood malaria in Africa" (preprint forthcoming on medRxiv). Malaria data were previously published by Snow et al. (2017) and are available online; climate data are too large for Github but again available from other sources.

All R scripts to execute the data analysis and visualization are stored in the Pipeline directory:

📦Pipeline
 ┣ 📂A - Utility functions
 ┃ ┣ 📜A00 - Configuration.R
 ┃ ┣ 📜A01 - Utility code for calculations.R
 ┃ ┣ 📜A02 - Utility code for plotting.R
 ┃ ┗ 📜A03 - Prep data for estimation.R
 ┣ 📂B - Extract climate and prevalence data
 ┃ ┣ 📜B01 - Extract CRU data and temperature for model.R
 ┃ ┣ 📜B02 - Extract GCMs.R
 ┃ ┗ 📜B03 - Generate precipitation key.R
 ┣ 📂C - Model estimation
 ┃ ┣ 📜C01 - MainSpec.R
 ┃ ┗ 📜C02 - Bootstrap.R
 ┣ 📂D - Model sensitivity analyses and checks
 ┃ ┣ 📜D01 - Model sensitivity.R
 ┃ ┗ 📜D02 - Randomization tests.R
 ┣ 📂E - Estimate historical and future prevalence
 ┃ ┣ 📜E01 - Predict prevalence.R
 ┃ ┣ 📜E02 - Prevalence summaries.R
 ┃ ┣ 📜E03 - Extract historical data.R
 ┃ ┣ 📜E04 - Extract future data.R
 ┃ ┣ 📜E05 - Extract historical regionals.R
 ┃ ┗ 📜E06 - Extract future regionals.R
 ┣ 📂F - Figure generation for main text
 ┃ ┣ 📜F01 - Fig1 - Maps.R
 ┃ ┣ 📜F02 - Fig1 - Time series and assembly.R
 ┃ ┣ 📜F03 - Fig2 - Coefficients.R
 ┃ ┣ 📜F04 - Fig2 - Global time series.R
 ┃ ┣ 📜F05 - Fig2 - Assembly.R
 ┃ ┣ 📜F06 - Fig3 - Maps.R
 ┃ ┣ 📜F07 - Fig3 - Elevation and latitude.R
 ┃ ┣ 📜F08 - Fig3 - Time series.R
 ┃ ┣ 📜F09 - Fig3 - Assembly.R
 ┃ ┣ 📜F10 - Fig4 - Maps.R
 ┃ ┣ 📜F11 - Fig4 - Elevation and latitude.R
 ┃ ┣ 📜F12 - Fig4 - Time series.R
 ┃ ┗ 📜F13 - Fig4 - Assembly.R
 ┣ 📂G - Figure generation for supplement
 ┃ ┣ 📜G01 - Visualize thermal curve expectations and data.R
 ┃ ┣ 📜G02 - Historical partials.R
 ┃ ┣ 📜G03 - Future partials.R
 ┃ ┣ 📜G04 - Attributable map.R
 ┃ ┗ 📜G05 - Projections map.R
 ┗ 📂H - Summary statistics for main text
 ┃ ┣ 📜H01 - Thermal responses.R
 ┃ ┣ 📜H02 - Historical summary.R
 ┃ ┣ 📜H03 - Future summary.R
 ┃ ┗ 📜H04 - Global warming levels.R