Code and public data for "Challenges in real-time prediction of infectious disease: a case study of dengue in Thailand"
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README.md

README.md

Predicting Dengue Fever in Thailand, 2014

This repository houses code and public data for the manuscript "Challenges in real-time prediction of infectious disease: a case study of dengue in Thailand". This paper describes a practical computational infrastructure that generated multi-step predictions of dengue incidence in Thai provinces every two weeks throughout 2014.

Due to restrictions in the data-sharing agreement with the owners of the case data from Thailand, we are not permitted to make the case data available on this repository. However, we have provided the code used in the analysis, the reproducible manuscript documents (although they are not fully reproducible as is here due to dependencies on data that we are not allowed to share), and the forecasts generated by our prediction model.

The code folder houses code for analysis and figure making.

The data folder contains csv files containing summaries of our forecasts.

The manuscript folder contains the dynamic document used to create the final manuscript and supplement that were submitted for review.