https://github.com/mrc-ide/safir

squire and friends individual rewrite
https://github.com/mrc-ide/safir

Last synced: 10 days ago
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squire and friends individual rewrite

• Host: GitHub
• URL: https://github.com/mrc-ide/safir
• Owner: mrc-ide
• License: other
• Created: 2021-03-24T11:15:58.000Z (almost 4 years ago)
• Default Branch: main
• Last Pushed: 2023-09-01T11:47:01.000Z (over 1 year ago)
• Last Synced: 2024-11-06T02:31:38.721Z (about 2 months ago)
• Language: R
• Homepage: https://mrc-ide.github.io/safir/
• Size: 341 MB
• Stars: 1
• Watchers: 5
• Forks: 2
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# **safir**

[![R build

status](https://github.com/mrc-ide/safir/workflows/R-CMD-check/badge.svg)](https://github.com/mrc-ide/safir/actions)

[![CodeFactor](https://www.codefactor.io/repository/github/mrc-ide/safir/badge)](https://www.codefactor.io/repository/github/mrc-ide/safir)

[![codecov.io](https://codecov.io/github/mrc-ide/safir/coverage.svg?branch=main)](https://codecov.io/github/mrc-ide/safir?branch=main)

**safir**: **s**quire **a**nd **f**riends **i**ndividual **r**ewrite

(and maintains the squire naming

[theme](https://en.wikipedia.org/wiki/Knights_of_the_Round_Table#Safir)).

It uses the [`{individual}`](https://github.com/mrc-ide/individual)

package to specify and run the simulation.

**safir** can run individual based stochastic versions of the **squire** and

**nimue** models, which recover trajectories from those aggregated population

models (see package vignettes). It also implements a model for vaccination

with an arbitrary number of doses and antibody titre dynamics which affect

protective efficacy as well as efficacy against severe disease outcomes.

Because **safir** implements multiple models as individual based simulations,

there is a large amount of code, but the central disease progression is shared

across the models within **safir**. Each vignette describes how the simulation

functions and where the relevant code can be found.

## Installation

``` r

install_github('mrc-ide/safir')

library(safir)

```

## Documentation

[`{safir}`](https://github.com/mrc-ide/safir) is documented on a

[dedicated website](https://mrc-ide.github.io/safir).

This includes the following vignettes:

-   **`Squire Validation Run`**: comparison of

    [`{safir}`](https://github.com/mrc-ide/safir) to

    [`{squire}`](https://github.com/mrc-ide/squire).

-   **`Nimue Validation Run`**: comparison of

    [`{safir}`](https://github.com/mrc-ide/safir) to

    [`{nimue}`](https://github.com/mrc-ide/nimue).

-   **`Vaccine model with multiple doses`**: runs the model for

    explicit tracking of antibody titre for a 2 dose vaccine.

-   **`Natural Immunity`**: demonstrates how to modify the vaccine model

    to also include mechanistic incorporation of natural immunity

    from infection, as opposed to a generic R (recovered) class.

-   **`Modeling of antibody titre and immunity`**: describes how antibody

    titre and protection against infection and severe disease is modeled.

-   **`Differential modeling of infection and vaccine derived NATs`**: is a short

    description of how to model differential boost/decay of vaccine and infection

    derived neutralizing antibody titres.

    

## License

MIT © Imperial College of Science, Technology and Medicine