https://github.com/samuelbrand1/monkeypoxuk

Some code for monkeypox
https://github.com/samuelbrand1/monkeypoxuk

Last synced: 2 months ago
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Some code for monkeypox

• Host: GitHub
• URL: https://github.com/samuelbrand1/monkeypoxuk
• Owner: SamuelBrand1
• License: mit
• Created: 2022-05-31T09:26:22.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2023-01-24T17:05:34.000Z (over 2 years ago)
• Last Synced: 2025-02-14T09:15:28.242Z (3 months ago)
• Language: Julia
• Size: 1.07 GB
• Stars: 10
• Watchers: 4
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# 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](https://ourworldindata.org/monkeypox) and [UKHSA technical briefings](https://www.gov.uk/government/publications/monkeypox-outbreak-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_](https://www.medrxiv.org/content/10.1101/2022.08.15.22278788v1).

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_](https://www.researchsquare.com/article/rs-2162921/v1).

### Quick start for inference

1. Download [Julia](https://julialang.org/downloads/).

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



Posterior means and 10-90% posterior probabilities 

### 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.