SSI fellowship application

# SSI fellowship application
## Paper -> Code -> Software
### Sam Abbott (@seabbs)
### University of Bristol

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# Outline

## 1. Who am I?

## 2. What do I do?

## 3. What would I do with the fellowship?

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# Who am I?
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# Background

* Postdoctoral researcher in infectious disease dynamics.1

* PhD: Modelling tuberculosis and the optimal usage of the BCG vaccination.2

* Previously: Mathematics, theoretical physics, applied mathematics, and data science in finance.

* Currently: Modelling zoonotic tuberculosis burden and actively looking for new research ideas/funding.

.footnote[
[1] More detail here: [https://www.samabbott.co.uk](https://www.samabbott.co.uk/)
[1] Thesis (in bookdown): [bit.ly/seabbs-thesis](http://bit.ly/seabbs-thesis)
] 
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# Interests

* Infectious disease dynamics.

* Improving infectious disease modelling practice and scientific workflow more generally.

* Informing policy and enabling others to do so in a more robust manner.

* Engaging the wider community with science and actively involving them where possible.

* Next section for more.

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# What do I do?

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# Statistical and mathematical modelling (Code > Paper)1

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# Software: `{getTBinR}`1, 2, 3

.footnote[
[1] Package Docs: [bit.ly/getTBinR](https://bit.ly/getTBinR), 
[2] JOSS paper: [bit.ly/getTBinR-paper](http://bit.ly/getTBinR-paper)
[3] Blog: [github.com/seabbs/hpru-blog-post-getTBinR](https://github.com/seabbs/hpru-blog-post-getTBinR)
]
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# Software: `{idmodelr}`1

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# Co-organiser of BristolR and speaker

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# Presenting

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# Blogging on R, modelling, software, etc.1

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# #rstats twitter1

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# What would I do with the fellowship?

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# Raising the profile of software > code > papers

* Infectious disease modelling community has varying levels of reproducibility, code quality and software development.

* Code is often not shared at all.

* Even if researchers have the best intentions code can be difficult to use.

* There maybe little documentation, no testing, and no long term support.

* Keen to form a community of best practice for infectious disease modellers. Most often it is not about not wanting to produce reusable code but about not knowing how.

* Often there is little acknowledgement of efforts to be reproducible and develop software (reviewers frequently do not look at code). Recognition from the SSI would be a great way of acknowledging the value of this input.

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# Running a hackathon for infectious disesase modelling tool development

* Soon to be attending a health economics hackathon that aims to teach the community about software best practices and also develop tools with the input of domain experts.

* Would like to replicate this for infectious disease modelling.

* Key aim would be to build out the community around `{idmodelr}` but any other tooling would be treated on a equal footing.

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# Expanding my horizons.

* I feel well versed in what constitutes good R software.

* I know very little about wider best practices or best practices in other languages.

* Aim is to use this fellowship as a chance to connect with a broader community and feedback my findings to infectious disease modellers using R and the wider R community.

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# Paper -> Code -> Software

## Slides: [bit.ly/seabbs-ssi](http://bit.ly/seabbs-ssi)

## Slide code:  [bit.ly/seabbs-ssi-code](http://bit.ly/seabbs-ssi-code)

## Use my stuff: [github.com/seabbs](https://www.github.com/seabbs)

## Read  my stuff: [samabbott.co.uk](https://www.samabbott.co.uk)

## Tweet at me: [@seabbs](https://twitter.com/seabbs)