pratikunterwegs / epidemics.jl

Julia package to model epidemic scenarios; a translation of the R(cpp) package {epidemics}.

Hello there! 👋

I'm a research software engineer working on epidemic modelling and pandemic preparedness.

I was previously a field ecologist working with animal spatial trajectory data, species distribution data and individual based simulation models for my PhD in ecology and evolution.

My current and past projects are distributed across personal and organisation repositories.

Project	Years	Link
PhD	2018 - 2022	@marmgroup
Epiverse-TRACE	2022 - 2024	@epiverse-trace

epidemics.jl's Issues

Implement final size calculation

This PR is to request the implementation of a final size calculation function from the output of an epidemic model, i.e., the data frame resulting from a call to epidemic(). This function should allow lumping or splitting by demographic group.

Argument checking for the default model

This PR is to request a function that checks the arguments to epidemic() for compatibility with the default model, seir!. This should include checking that there are only single pathogen parameters, even though pathogens can be initialised with multiple parameters.

Retire epidemic() function

This issue is to request that the epidemic() function should be retired in favour of separate model functions, such as epidemic_default().

Separate default model from epidemic()

This issue is to request that the default model be renamed to epidemic_default() and separated out from the overall epidemic() function, with standalone input checking suitable for this model.

Add the Vacamole model

This issue is to request addition of the RIVM Vacamole Covid-19 model to Epidemics.jl. This should mirror the implementation in {epidemics}.

Implement SEIR-V model

This PR is to request that the default model in Epidemics.jl be updated to include an optional vaccination regime to mirror the default model in {epidemics}.

Implement overlapping interventions

This issue is to request a way to concatenate interventions and apply the combined intervention with age-specific effects to the default model (and by extension any model with age structured social contacts). See the equivalent implementation in {epidemics}.

Main function should mirror epidemics::epidemic()

This PR is to request that the main function, epidemic(), should mirror the R function epidemics::epidemic(), and allow passing arguments as ... or the Julia equivalent. These should then be checked and prepared by the appropriate functions, chosen based on the model chosen in epidemic(model = ...), before being passed to a function specified by model = ....

Add vaccination regime class

This PR is to request a vaccination regime type Vaccination that mirrors epidemics::vaccination() from {epidemics}.

Implement multi-dose vaccinations

This issue is to request the implementation of multi-dose vaccination regimes in any model with more than one vaccination compartment. This should happen concurrently with addition of a two-dose vaccination model. See the equivalent issue for implementation of multi-dose vaccination in {epidemics}.