will-s-hart/climate-vbd-uncertainty


Python code and data accompanying Hart et al., “Internal climate variability amplifies the need for vector-borne disease outbreak preparedness”, PNAS, 2025 (https://doi.org/10.1073/pnas.2507311122).

This repository contains:

• —Code for reproducing the figures in the manuscript ('paper_code' directory).
• —Code for the author-developed climepi package (version 0.5.3) used in the analyses ('climepi' directory). This package is also distributed via conda-forge (see the package's main repository at https://github.com/idm-oxford/climate-epidemics).
• —Climate projection and recorded temperature data used in the analyses ('data' directory).
• —Results of the literature search reported in the Supporting Information of the manuscript ('literature_search' directory).
• —Source code for a web app available at https://idm-oxford.github.io/climate-vbd-uncertainty-paper/, which is hosted on Hugging Face spaces ('app_code' directory).

To reproduce the figures, download the source code and create a `conda` virtual environment named 'climate-vbd-uncertainty' with the required dependencies:

climate-vbd-uncertainty-paper $ conda env create -f environment.yml

Or alternatively, using mamba (may be faster):

climate-vbd-uncertainty-paper $ mamba env create -f environment.yml

The figures (in SVG format) can then be reproduced by executing the notebooks in the 'paper_code' directory using the 'climate-vbd-uncertainty' environment created in the above step.

Alternatively, all figures can be reproduced using `snakemake`:

climate-vbd-uncertainty-paper $ conda activate climate-vbd-uncertainty
(climate-vbd-uncertainty) climate-vbd-uncertainty-paper $ snakemake --cores 1 --forceall figures_svg

Note that the Google Chrome browser must be installed in order to export the figures to SVG.

If Inkscape is installed, PNG and PDF figures can be created by running

(climate-vbd-uncertainty) climate-vbd-uncertainty-paper $ snakemake --cores 1