Note
This is an example contest repo for the SPHERE-PPL forecasting events. It will have all of the information sections you will find in active contests and will mostly follow the same rules/timelines. We have included example analysis and outputs to help guide new entrants.
Introduction 1
Mpox is an infectious disease that can cause a painful rash, enlarged lymph nodes, fever, headache, muscle ache, back pain and low energy. Most people fully recover, but some get very sick.
Mpox is caused by the monkeypox virus (MPXV). It is an enveloped double-stranded DNA virus of the Orthopoxvirus genus in the Poxviridae family, which includes variola, cowpox, vaccinia and other viruses. There are two distinct clades of the virus: clade I (with subclades Ia and Ib) and clade II (with subclades IIa and IIb).
A global outbreak of clade IIb began in 2022 and continues to this day, including in some African countries. There are also growing outbreaks of clades Ia and Ib affecting the Democratic Republic of the Congo and other countries in Africa. As of August 2024, clade Ib has also been detected beyond Africa.
The natural reservoir of the virus is unknown, but various small mammals such as squirrels and monkeys are susceptible.
The dataset included in this forecasting contest covers the period from Jan 2022 to July 2024.
This contest has its own repository with pre-prepared data (found in the data folder) and a template report (mpox_report.qmd) which showcases how to load the data, perform analyses and then export results into the correct format. There is also be a folder for any additional scripts that are required.
For this example contest, we are looking to forecast monthly regional case numbers for the 6 WHO regions (African, Eastern Mediterranean, European, Region of the Americas, South-East Asia, Western Pacific) for the remainder of 2024 (August-December).
The contest repo can be found here: Contest-Example-Mpox.
The simplest way to get started is to fork this repo and then clone it onto your local machine. This will allow the organisers to see the forks and keep track of entrants. Alternatively, you can download the repo manually and get started. Each entry must be uploaded to a public github repo to be considered (see Rules below)
- Any coding languages are allowed but all analyses must be reproducible by the panel.
- All entries must be loaded into a public Github repo.
- All entries must follow the submission formats outlined below.
- All entries must include a max 1000 word report to accompany the forecast analyses. This can be as a separate PDF/hmtl or incorporated into a quarto/jupyter notebook.
We are in the process of building back-end architecture to automatically find all forked repos and enter them into the contest but in the interim, please send an email to contest@sphere-ppl.org with a link to the public github repo.
The entries should be saved in the submission folder with the forecast estimates saved as a csv (i.e. forecast.csv) and the report saved as a pdf, html or a quarto md (i.e. report.pdf, report.html or report.qmd). The forecast estimates must contain three columns: WHO region, month start date and Estimate (see example in the repo).
This contest has a page on our SPHERE-PPL Zulip where teams can message and get clarification/advice. We will also be monitoring the contest repo. Regular updates will be posted on both platforms.
Unless otherwise noted, the content in this repository is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
For the data sets in the data/ folder, please see data/README.md for the applicable copyrights and licenses.
Footnotes
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Adapted from WHO Mpox Dashboard (https://worldhealthorg.shinyapps.io/mpx_global/) ↩