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https://github.com/harmonydata/harmony_examples
Example Jupyter notebook and R scripts using Harmony in real research problems
https://github.com/harmonydata/harmony_examples
data data-harmonisation data-harmonization harmonisation psychology python r research
Last synced: 22 days ago
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Example Jupyter notebook and R scripts using Harmony in real research problems
- Host: GitHub
- URL: https://github.com/harmonydata/harmony_examples
- Owner: harmonydata
- License: mit
- Created: 2024-11-19T06:40:47.000Z (about 2 months ago)
- Default Branch: main
- Last Pushed: 2024-12-17T10:50:33.000Z (24 days ago)
- Last Synced: 2024-12-17T11:37:37.703Z (24 days ago)
- Topics: data, data-harmonisation, data-harmonization, harmonisation, psychology, python, r, research
- Language: HTML
- Homepage: https://harmonydata.ac.uk/
- Size: 200 KB
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
[](https://twitter.com/harmony_data)
# Harmony example scripts
Harmony is a tool using AI which allows you to compare items from questionnaires and identify similar content. You can try Harmony at https://harmonydata.ac.uk/app and you can read our blog at https://harmonydata.ac.uk/blog/.
Here you can find example scripts for using the Python and R libraries.
## R examples
* Walkthrough R notebook in R Studio: 
* Walkthrough R notebook in Google Colab: 
[View the PDF documentation of the R package on CRAN](https://cran.r-project.org/web/packages/harmonydata/harmonydata.pdf)
* R Markdown to Check for Correspondence between Differently Worded Versions of the Same Scale Item View on Github - credit to [Deanna Varley](https://harmonydata.ac.uk/matilda/)
* R Script to Check for Matches between Items from Different Scales View on Github - credit to [Deanna Varley](https://harmonydata.ac.uk/matilda/)
## Python examples
* Walkthrough Python notebook in [Google Colab](https://colab.research.google.com/github/harmonydata/harmony/blob/main/Harmony_example_walkthrough.ipynb) with a single click:
* [Example script to create a crosswalk table on real survey data](./create_harmony_crosswalks_in_python.ipynb)
* [Example script to strip prefixes from questions](./strip_common_prefixes_from_questions.ipynb)
## 🖱 Looking to try Harmony in the browser?
Visit: https://harmonydata.ac.uk/app/
## Looking for Harmony source code?
Harmony is based on four repositories: the core Python library, the API, the R port, and the front end for running in the browser. We welcome contributions and you can raise issues, pick up issues, and make pull requests.
* [Python](https://github.com/harmonydata/harmony) - the main core library and the Python package which is on [Pypi](https://pypi.org/project/harmonydata/)
* [R](https://github.com/harmonydata/harmony_r) - the R port is on [CRAN](https://cran.r-project.org/web/packages/harmonydata/index.html) and it is slightly less mature than Python so we really appreciate if you can give the R package some TLC.
* [API](https://github.com/harmonydata/harmonyapi) - the Python API runs with Pydantic and Fast API and is running on an on-prem server enabling the web app to work
* [Web front end](https://github.com/harmonydata/app) - we welcome feedback and contributions on front end and UX issues
* If you're doing research and found Harmony useful, please [cite us](/ai-in-mental-health/bmc-psychiatry-paper/)!
* If you're a researcher trying to use the tool, and you encounter a problem, a bug, or a feature which you would like us to implement, please [raise an issue on Github](https://github.com/harmonydata/harmony) or [message us on Discord](https://discord.gg/harmonydata).
[Read our guide to contributing to Harmony here](https://harmonydata.ac.uk/contributing-to-harmony/) or read [CONTRIBUTING.md](https://github.com/harmonydata/harmony/blob/main/CONTRIBUTING.md).
## 🖥 Installation instructions for Python library (video)
[](https://www.youtube.com/watch?v=enWh0-4I0Sg "Installing Harmony")
## Who to contact?
You can contact Harmony team at https://harmonydata.ac.uk/, or Thomas Wood at https://fastdatascience.com/.
## 😃💁 Who worked on Harmony?
Harmony is a collaboration project between [Ulster University](https://ulster.ac.uk/), [University College London](https://ucl.ac.uk/), the [Universidade Federal de Santa Maria](https://www.ufsm.br/), and [Fast Data Science](http://fastdatascience.com/). Harmony has been funded by [Wellcome](https://wellcome.org/) as part of the [Wellcome Data Prize in Mental Health](https://wellcome.org/grant-funding/schemes/wellcome-mental-health-data-prize) and by [Economic and Social Research Council (ESRC)](https://www.ukri.org/councils/esrc/).
The core team at Harmony is made up of:
* [Dr Bettina Moltrecht, PhD](https://profiles.ucl.ac.uk/60736-bettina-moltrecht) (UCL)
* [Dr Eoin McElroy](https://www.ulster.ac.uk/staff/e-mcelroy) (University of Ulster)
* [Dr George Ploubidis](https://profiles.ucl.ac.uk/48171-george-ploubidis) (UCL)
* [Dr Mauricio Scopel Hoffmann](https://ufsmpublica.ufsm.br/docente/18264) (Universidade Federal de Santa Maria, Brazil)
* [Thomas Wood](https://freelancedatascientist.net/) ([Fast Data Science](https://fastdatascience.com))
## 📜 License
MIT License. Copyright (c) 2023 Ulster University (https://www.ulster.ac.uk)
## 📜 How do I cite Harmony?
You can cite our validation paper:
McElroy, Wood, Bond, Mulvenna, Shevlin, Ploubidis, Scopel Hoffmann, Moltrecht, [Using natural language processing to facilitate the harmonisation of mental health questionnaires: a validation study using real-world data](https://bmcpsychiatry.biomedcentral.com/articles/10.1186/s12888-024-05954-2#citeas). BMC Psychiatry 24, 530 (2024), https://doi.org/10.1186/s12888-024-05954-2
A BibTeX entry for LaTeX users is
```
@article{mcelroy2024using,
title={Using natural language processing to facilitate the harmonisation of mental health questionnaires: a validation study using real-world data},
author={McElroy, Eoin and Wood, Thomas and Bond, Raymond and Mulvenna, Maurice and Shevlin, Mark and Ploubidis, George B and Hoffmann, Mauricio Scopel and Moltrecht, Bettina},
journal={BMC psychiatry},
volume={24},
number={1},
pages={530},
year={2024},
publisher={Springer}
}
```
