https://github.com/tommonks/des_sharing_lit_review
Systematic scoping review paper for healthcare DES model sharing.
https://github.com/tommonks/des_sharing_lit_review
discrete-event-simulation health health-economics healthcare open-models open-science operational-research reproducibility reproducible-paper reproducible-research reproducible-science
Last synced: 5 months ago
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Systematic scoping review paper for healthcare DES model sharing.
- Host: GitHub
- URL: https://github.com/tommonks/des_sharing_lit_review
- Owner: TomMonks
- License: mit
- Created: 2022-12-06T20:21:06.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-06-05T16:07:00.000Z (about 2 years ago)
- Last Synced: 2025-09-05T02:38:37.447Z (9 months ago)
- Topics: discrete-event-simulation, health, health-economics, healthcare, open-models, open-science, operational-research, reproducibility, reproducible-paper, reproducible-research, reproducible-science
- Language: HTML
- Homepage: https://tommonks.github.io/des_sharing_lit_review/
- Size: 10.4 MB
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](https://opensource.org/licenses/MIT)
[](https://mybinder.org/v2/gh/TomMonks/des_sharing_lit_review/HEAD)
[](https://www.python.org/downloads/release/python-390/)
[](https://tommonks.github.io/des_sharing_lit_review)
[](https://orcid.org/0000-0001-5274-5037)
[](https://orcid.org/0000-0003-2631-4481)
# Computer model and code sharing practices in healthcare discrete-event simulation: a systematic scoping review
## Overview
The materials and data in this repository support: Harper and Monks (2023). [Computer model and code sharing practices in healthcare discrete-event simulation: a systematic scoping review](https://doi.org/10.1080/17477778.2023.2260772). All materials are published under an [MIT permissive license](https://github.com/TomMonks/des_sharing_lit_review/blob/main/LICENSE).
## Author ORCIDs
[](https://orcid.org/0000-0001-5274-5037)
[](https://orcid.org/0000-0003-2631-4481)
## Write up of study
Methods, results, and code are available in our online Jupyter Book [https://tommonks.github.io/des_sharing_lit_review](https://tommonks.github.io/des_sharing_lit_review)
A full write-up of the work is available **open access** in the Journal of Simulation. If you use this work please cite the paper.
> Monks, T., & Harper, A. (2023). Computer model and code sharing practices in healthcare discrete-event simulation: a systematic scoping review. Journal of Simulation, 1–16. https://doi.org/10.1080/17477778.2023.2260772
**Bibtex citation:**
```bibtex
@article{monks_harper_2023,
author = {Thomas Monks and Alison Harper},
title = {Computer model and code sharing practices in healthcare discrete-event simulation: a systematic scoping review},
journal = {Journal of Simulation},
pages = {1--16},
year = {2023},
publisher = {Taylor \& Francis},
doi = {10.1080/17477778.2023.2260772},
URL = {https://doi.org/10.1080/17477778.2023.2260772},
eprint = {https://doi.org/10.1080/17477778.2023.2260772}
}
```
## Aim and research questions:
The overarching research aim is determine to what extent authors of DES health studies share models and where models are shared how is this done.
### Primary research questions
1. What proportion of DES healthcare studies share code?
2. How is sharing affected by FOSS, Covid-19, publication type and year of publication?
3. What proportion of studies make use of a reporting guideline?
4. What methods, tools, and resources did authors use to share their computer models and code?
5. To what extent do the DES health community follow best practice for open science when sharing computer models?
6. To what extent can the healthcare DES community improve its sharing of computer models?
## Dependencies
[](https://www.python.org/downloads/release/python-390/)
All dependencies can be found in [`binder/environment.yml`]() and are pulled from conda-forge. To run the code locally, we recommend install [mini-conda](https://docs.conda.io/en/latest/miniconda.html); navigating your terminal (or cmd prompt) to the directory containing the repo and issuing the following command:
> `conda env create -f binder/environment.yml`
**Online Alternatives**:
* Visit our [jupyter book]((https://tommonks.github.io/des_sharing_lit_review) for interactive code and explanatory text
* Run out Jupyter notebooks in binder [](https://github.com/TomMonks/des_sharing_lit_review/main)
## Repo overview
```bash
.
├── binder
│ └── environment.yml
├── CITATION.cff
├── content
│ ├── 01_intro
│ ├── 02_methods
│ ├── 03_results
│ ├── 04_discussion
│ └── 04_prisma
├── data
├── LICENSE
├── README.md
├── _config.yml
└── _toc.yml
```
* `binder` - contains the environment.yml file (des_review) and all dependencies managed via conda.
* `CITATION.cff` - citation information for GitHub repository.
* `content` - the analysis notebooks and markdown arranged by introductory, methods, results, and PRISMA reporting checklist chapters.
* `data` - directory containing data files used by analysis notebooks.
* `LICENSE` - details of the MIT permissive license of this work.
* `README` - what you are reading now!
* `_config.yml` - configuration of our Jupyter Book.
* `_toc.yml` - the table of contents for our Jupyter Book.
## Study data
All study data is contained within this repository. It can be found in the `data` sub-directory.
**Main data files:**
* `share_sim_data_extract.zip`: main study data stored as a CSV. It includes all publications carried forward to the data extraction phase.
* `bp_audit.zip`: Contains the studies and additional data extraction used within the best practice audit of shared computer models.
## Testing
If any updates to the data are made we recommend re-running the [Data source testing notebook](https://github.com/TomMonks/des_sharing_lit_review/blob/main/content/03_results/12_data_testing_bkp.ipynb). This will perform a set of tests on the main and best practice audit datasets to check that data is in the correct place and format.