This repository contains the data and code for our paper:
Toshiaki R. Asakura, Sung-mok Jung, Hiroaki Murayama, Cyrus Ghaznavi, Haruka Sakamoto, Ayaka Teshima, Fuminari Miura, Akira Endo (2024). Projecting international mpox spread in Asia: ongoing global health risk. medRxiv [Preprint]. doi: 10.1101/2024.04.17.24305832
Note: Since the intermediate files for reproducing figures/tables are very large and we cannot upload international flight volume data, some code will cause errors. Therefore, this repository is prepared for the implementation part to be checked.
Our fitting process and simulations with meta-population model used the following data sets.
- Line list of mpox incidence in Japan:
/data/JPN_linelist/master_20230707.csv. - International flight volume data:
/data/flight/selected_flight_matrix.csv(not uploaded). - Population size in each country:
/data/pop_size_edit.csv.
Clone this repository and type docker compose up to
install the Docker image and to set up the container.
Then, you can run the code in script via Jupyter Lab.
Run code in a sequence following the number of prefix of each file in script directory.
It takes around 1-2 days to complete each scenario in 2j_AFP_MCMC.jl, and this file will cause an error because of lacking international flight volume data.
3j_prepare_data_for_vis.jl prepared the necessary files for the visualisation. Outputs from 3j file were uploaded in tmp_results and with thouse outputs, you can run 4j, 5r, 6r and 7p files to reproduce our results.