STARS Work Package 1 Summary

Summary of the six computational reproducibility assessments conducted as part of STARS Work Package 1.

Table of contents

• 👋 About the repository
• 📍 Locating tables and figures from the article
• 📖 View book locally
• 📝 Citation
• 💰 Funding

👋 About the repository

In work package 1, we assessed the computational reproducibility of eight discrete-event simulation papers with models in Python and R. The reproductions and findings are summarised at: https://pythonhealthdatascience.github.io/stars_wp1_summary/.

Relevant GitHub repositories:

Repository	Description
stars-reproduction-protocol	Latex files for reproduction protocol
stars-reproduce-allen-2020	Test run of reproducibility protocol on Allen et al. 2020
stars-reproduction-template	Template for assessment of computational reproducibility
stars-reproduce-shoaib-2022	Reproduction study 1: Shoaib and Ramamohan 2022 (Python)
stars-reproduce-huang-2019	Reproduction study 2: Huang et al. 2019 (R)
stars-reproduce-lim-2020	Reproduction study 3: Lim et al. 2020 (Python)
stars-reproduce-kim-2021	Reproduction study 4: Kim et al. 2021 (R)
stars-reproduce-anagnostou-2022	Reproduction study 5: Anagnostou et al. 2022 (Python)
stars-reproduce-johnson-2021	Reproduction study 6: Johnson et al. 2021 (R)
stars-reproduce-hernandez-2015	Reproduction study 7: Hernandez et al. 2015 (Python + R)
stars-reproduce-wood-2021	Reproduction study 8: Wood et al. 2021 (R)

📍 Locating tables and figures from the article

Figure/Table	Method	Location
Figure 1. Five standards that scientific code should strive to achieve, and the benefits of doing so	Inkscape	images/5rs.svg
Figure 2. Time to complete items in scope for each reproduction, inspired by figure in Krafczyk et al. 2021	Matplotlib	Created within pages/reproduction.qmd, saved as images/article_times.png
Figure 3. Recommendations to support reproduction, with stars to highlight five recommendations considered to have the greatest potential impact.	Inkscape	images/reproduction_wheel.svg
Figure 4. Recommendations to support troubleshooting and reuse	Inkscape	images/troubleshooting_wheel.svg
Figure 5. Of the eight healthcare DES studies evaluated, proportion that met each recommendation in the current STARS framework.	Plotly express	Created within pages/repo_evaluation.qmd, saved as images/stars_criteria.png
Figure 6. Of the eight healthcare DES studies evaluated, proportion that met each item in the current STRESS-DES criteria.	Plotly express	Created within pages/paper_evaluation.qmd, saved as stress_criteria.png
Figure 7. Of the eight healthcare DES studies evaluated, proportion that met each criteria in the general reporting checklist for DES	Plotly express	Created within pages/paper_evaluation.qmd, saved as ispor_criteria.png
Table 2. Evaluation of repositories against ACM badge criteria.	-	Created within pages/repo_evaluation.qmd, saved as data/badges_table.csv (and Table 2 is an extract from that table)
Table 3. Proportion of applicable criteria that were fully met, from evaluation of repository or article, alongside the proportion of items reproduced from each study.	-	Combination of two tables: (1) data/applicable_stars.csv created within pages/repo_evaluation.qmd, and (2) data/applicable_report.csv created within pages/paper_evaluation.qmd
Table D1. Evaluation of studies against badge criteria - grouped into three themes, as defined by NISO.	-	Created within pages/repo_evaluation.qmd, saved as data/badges_table.csv

The remaining tables were created directly in the Latex article, rather than in this repository, as they are not describing results from reproduction:

• Table 1. Description of the included studies.
• Table 4. Simple checklists to assist reviewers in assessing the openness, longevity, and reproducibility of DES models during peer review.
• Table B1. Links for reproduction and evaluation.
• Table B2. Links to original study repositories.

📖 View book locally

The website is a quarto book hosted with GitHub pages. If you want to view the book locally on your own machine you will need to:

1. Clone GitHub repository

git clone https://github.com/pythonhealthdatascience/stars_wp1_summary.git

2. Create the virtual environment

virtualenv stars_wp1_summary
source stars_wp1_summary/bin/activate
pip install -r requirements.txt

3. Create the book

quarto render

4. Open the book in your browser (open the _book/index.html file).

📝 Citation

This repository has been archived on Zenodo and can be cited as:

Heather, A., Monks, T., & Harper, A. (2024). STARS Work Package 1 Summary. Zenodo. https://doi.org/10.5281/zenodo.14267268.

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

Member	ORCID	GitHub
Amy Heather		https://github.com/amyheather
Thomas Monks		https://github.com/TomMonks
Alison Harper		https://github.com/AliHarp

💰 Funding

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