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https://github.com/pythonhealthdatascience/stars-reproduce-allen-2020

Test-run of our reproducibility protocol on Allen et al. 2020
https://github.com/pythonhealthdatascience/stars-reproduce-allen-2020

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Test-run of our reproducibility protocol on Allen et al. 2020

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README 

        
# STARS: Computational reproducibility of Allen et al. 2020 STARS



[![Valid CITATION.cff](https://github.com/pythonhealthdatascience/stars-reproduce-allen-2020/actions/workflows/cff_validation.yaml/badge.svg)](https://github.com/pythonhealthdatascience/stars-reproduce-allen-2020/actions/workflows/cff_validation.yaml)



⚠️ ***This is a test-run for STARS work package 1 using a paper that Tom Monks was involved with. It was created to help us test out the reproduction protocol and guide creation of the [template repository](https://github.com/pythonhealthdatascience/stars_reproduction_template).*** ⚠️



This repository forms part of work package 1 on the project STARS: Sharing Tools and Artefacts for Reproducible Simulations. It assesses the computational reproducibility of:



> Allen, M., Bhanji, A., Willemsen, J., Dudfield, S., Logan, S., & Monks, T. **A simulation modelling toolkit for organising outpatient dialysis services during the COVID-19 pandemic**. *PLoS One* 15, 8 (2020). 



## Website



⭐ **[Click here to check out the website for this repository](https://pythonhealthdatascience.github.io/stars-reproduce-allen-2020/)** ⭐



This website is created using Quarto and hosted using GitHub Pages. It shares everything from this computational reproducibility assessment, displaying:

* The original study article and associated artefacts.

* Code and documentation from reproduction of the model.

* Evaluation of model reproduction success.

* Evaluation of the original study against guidelines for sharing research, criteria for journal reproducibility guidelines, and article reporting guidelines.

* Logbook with chronological entries detailing reproduction work.

* Final report describing the computational reproducibility assessment.



## Protocol



The protocol for this work is summarised in the diagram below and archived on Zenodo: **Link to Zenodo once published**.



![Workflow](./quarto_site/stars_wp1_workflow.png)



## Repository overview



```bash

├── .github

│   └──  workflows

│        └──  ...

├── evaluation

│   └──  ...

├── logbook

│   └──  ...

├── original_study

│   └──  ...

├── quarto_site

│   └──  ...

├── reproduction

│   └──  ...

├── .gitignore

├── CHANGELOG.md

├── CITATION.cff

├── CONTRIBUTING.md

├── LICENSE

├── README.md

├── _quarto.yml

├── citation_apalike.apa

├── citation_bibtex.bib

├── index.qmd

└── requirements.txt

```



**Key sections:** This files have all the content related to the original study and reproduction...



* **`original_study/`** - Original study materials (i.e. journal article, supplementary material, code and any other research artefacts).

* **`reproduction/`** - Reproduction of the simulation model. Once complete, this functions as a research compendium for the model, containing all the code, parameters, outputs and documentation.

* **`evaluation/`** - Quarto documents from the evaluation of computational reproducibility. This includes the scope, assessment of reproduction success, and comparison of the original study materials against various guidelines, and summary report.

* **`logbook/`** - Daily record of work on this repository.



**Other sections:** The following files support creation of the Quarto site to share the reproduction, or are other files important to the repository (e.g. `README`, `LICENSE`, `.gitignore`)...



* `.github/workflows/` - GitHub actions.

* `quarto_site/` - A Quarto website is used to share information from this repository (including the original study, reproduced model, and reproducibility evaluation). This folder contains any additional files required for creation of the site that do not otherwise belong in the other folders.

* `.gitignore` - Untracked files.

* `CHANGELOG.md` - Description of changes between GitHub releases and the associated versions on Zenodo.

* `CITATION.cff` - Instructions for citing this repository, created using [CFF INIT](https://citation-file-format.github.io/).

* `CONTRIBUTING.md` - Contribution instructions for repository.

* `LICENSE` - Details of the license for this work.

* `README.md` - Description for this repository. You'll find a seperate README for the model within the `reproduction/` folder, and potentially also the `original_study/` folder if a README was created by the original study authors.

* `_quarto.yml` - Set-up instructions for the Quarto website.

* `citation_apalike.bib` - APA citation generated from CITATION.cff.

* `citation_bibtex.bib` - Bibtex citation generated from CITATION.cff.

* `index.qmd` - Home page for the Quarto website.

* `requirements.txt` - Environment for creation of Quarto site (used by `.github/workflows/quarto_publish.yaml`).



## Citation



If you wish to cite this repository, please refer to the citation file `CITATION.cff`, and the auto-generated alternatives `citation_apalike.apa` and `citation_bibtex.bib`.



## License



This repository is licensed under the [MIT License](https://github.com/pythonhealthdatascience/stars-reproduce-allen-2020/blob/main/LICENSE).



This is aligned with the original study, who also licensed their work under the [MIT License](https://github.com/pythonhealthdatascience/stars-reproduce-allen-2020/blob/main/original_study/dialysis-service-delivery-covid19-v1.0/LICENSE).



## Funding



This work is supported by the Medical Research Council [grant number MR/Z503915/1].