MonkeypoxUK

The MonkeypoxUK module provides methods for simulating MPX spread among men-who-have-sex-with-men (MSM) in the United Kingdom as well as the wider community. Weekly case data is from a combination of Global.Health/ourworldindata and UKHSA technical briefings.

A first preprint describing the underlying reasoning and methodology is now available The role of vaccination and public awareness in medium-term forecasts of monkeypox incidence in the United Kingdom.

A second preprint using data directly from the UKHSA, rather than open source data from Global.Health, and with an updated set of counter-factual scenarios is now available The role of vaccination and public awareness in forecasts of monkeypox incidence in the United Kingdom.

Quick start for inference

1. Download Julia.
2. Clone this repository.
3. Start the Julia REPL.
4. Change working directory to where this repo is cloned.
5. Enter Pkg mode by pressing ]
6. Activate the environment for MonkeypoxUK and download the underlying dependencies.

   pkg> activate .
   pkg> instantiate

7. The script mpx_inference.jl covers running the inference methodology. The script mpxv_datawrangling.jl loads the underlying case data into a two column matrix mpxv_wkly where rows are weeks and first column is reported MSM cases and second column is reported non-MSM cases. The Monday date for each week is given as a Vector{Date} array wks.

Latest case projections for the UK

<figure> <img src="plots/case_projections_2022-10-17.png" alt="Trulli" style="width:100%"> <figcaption align = "center"><b>Posterior means and 10-90% posterior probabilities </b></figcaption> </figure>

Method Update [15-09-2022]

We are transitioning to using a method for inferring GBMSM proportion among non-reporting individuals in the UKHSA reporting dataset. For results using the datasets described above (and in linked preprint) please refer to \plots_globalhealth and \posteriors_globalhealth.

Data update [26-09-2022]

The data set from Global.Health has now depreciated.