Chi
Chi: A Python package for treatment response modelling - Published in JOSS (2024)
Science Score: 98.0%
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 9 DOI reference(s) in README and JOSS metadata -
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Links to: joss.theoj.org -
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✓JOSS paper metadata
Published in Journal of Open Source Software
Keywords
Scientific Fields
Repository
Chi is an open source Python package which is designed for PKPD modelling and model-informed precision dosing (MIPD).
Basic Info
- Host: GitHub
- Owner: DavAug
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://doi.org/10.21105/joss.05925
- Size: 1.06 GB
Statistics
- Stars: 10
- Watchers: 1
- Forks: 5
- Open Issues: 34
- Releases: 7
Topics
Metadata Files
README.md
Chi
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About
Chi is an open source Python package for pharmacokinetic and pharmacodynamic (PKPD) modelling.
All features of the software are described in detail in the full API documentation.
Getting started
Installation
- Install sundials
Chi uses the open source package Myokit to solve ordinary differential equations and compute their sensitivities efficiently. Myokit does this using sundials' CVODESS, which needs to be installed with:
On Ubuntu:
bash apt-get install libsundials-devOn MacOS:
bash brew install sundialsOn Windows: No action required. Myokit will install sundial automatically.
- Install chi
bash pip install chi-drm
You can now use chi's functionality by importing it
python
import chi
### Tutorials
Tutorials and more detailed explanations on how to use chi can be found in the documentation's getting started section.
Citation
If you use this software in your work, please cite it using the following metadata:
Citation string
Augustin, D., (2024). Chi: A Python package for treatment response modelling. Journal of Open Source Software, 9(94), 5925, https://doi.org/10.21105/joss.05925
BibTeX
@article{
Augustin2024,
doi = {10.21105/joss.05925},
url = {https://doi.org/10.21105/joss.05925},
year = {2024},
publisher = {The Open Journal},
volume = {9},
number = {94},
pages = {5925},
author = {David Augustin},
title = {Chi: A Python package for treatment response modelling},
journal = {Journal of Open Source Software}
}
Contributing
There are lots of ways how you can contribute to Chi's development, and you are welcome to join in! For example, you can report problems or make feature requests on the issues pages.
Similarly, if you would like to contribute documentation or code you can create and issue, and then provide a pull request for review. To facilitate contributions, we have written extensive contribution guidelines to help you navigate the code.
License
Owner
- Name: David Augustin
- Login: DavAug
- Kind: user
- Website: davaug.github.io
- Repositories: 2
- Profile: https://github.com/DavAug
DPhil in Computer Science at the University of Oxford.
JOSS Publication
Chi: A Python package for treatment response modelling
Authors
Department of Computer Science, University of Oxford, Oxford, United Kingdom
Editor
Antonia Mey
Tags
pkpd treatment planning inference Bayesian inferenceCitation (CITATION.cff)
cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Augustin"
given-names: "David"
orcid: "https://orcid.org/0000-0002-4885-1088"
title: "Chi: A Python package for treatment response modelling"
version: 1.0.0
year: 2024
url: "https://github.com/DavAug/chi"
preferred-citation:
type: article
authors:
- family-names: "Augustin"
given-names: "David"
orcid: "https://orcid.org/0000-0002-4885-1088"
title: "Chi: A Python package for treatment response modelling"
version: 1.0.0
year: 2024
url: "https://doi.org/10.21105/joss.05925"
doi: "10.21105/joss.05925"
publisher: "The Open Journal"
journal: "Journal of Open Source Software"
volume: 9
number: 94
pages: 5925
GitHub Events
Total
- Watch event: 3
Last Year
- Watch event: 3
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| DavAug | d****n@g****t | 1,698 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 70
- Total pull requests: 46
- Average time to close issues: about 2 months
- Average time to close pull requests: about 1 month
- Total issue authors: 3
- Total pull request authors: 3
- Average comments per issue: 0.16
- Average comments per pull request: 0.96
- Merged pull requests: 43
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- DavAug (68)
- ns-rse (1)
- breisfeld (1)
Pull Request Authors
- DavAug (46)
- MichaelClerx (1)
- martinjrobins (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- kaleido *
- sphinx >=1.5,
- sphinx-rtd-theme *
- arviz >=0.11
- myokit >=1.33
- numpy >=1.17
- pandas >=0.24
- pints >=0.4
- plotly >=4.8.1
- tqdm >=4.46.1
- xarray >=0.19
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