gen_surv

gen_surv is a Python package for simulating survival data under a variety of models, inspired by the R package genSurv. It supports data generation for:

• Cox Proportional Hazards Models (CPHM)
• Continuous-Time Markov Models (CMM)
• Time-Dependent Covariate Models (TDCM)
• Time-Homogeneous Hidden Markov Models (THMM)

📦 Installation

poetry install

✨ Features

• Consistent interface across models
• Censoring support (uniform or exponential)
• Easy integration with pandas and NumPy
• Suitable for benchmarking survival algorithms and teaching
• Accelerated Failure Time (Log-Normal) model generator
• Command-line interface powered by Typer

🧪 Example

from gen_surv import generate

# CPHM
generate(model="cphm", n=100, model_cens="uniform", cens_par=1.0, beta=0.5, covar=2.0)

# AFT Log-Normal
generate(model="aft_ln", n=100, beta=[0.5, -0.3], sigma=1.0, model_cens="exponential", cens_par=3.0)

# CMM
generate(model="cmm", n=100, model_cens="exponential", cens_par=2.0,
         qmat=[[0, 0.1], [0.05, 0]], p0=[1.0, 0.0])

# TDCM
generate(model="tdcm", n=100, dist="weibull", corr=0.5,
         dist_par=[1, 2, 1, 2], model_cens="uniform", cens_par=1.0,
         beta=[0.1, 0.2, 0.3], lam=1.0)

# THMM
generate(model="thmm", n=100, qmat=[[0, 0.2, 0], [0.1, 0, 0.1], [0, 0.3, 0]],
         emission_pars={"mu": [0.0, 1.0, 2.0], "sigma": [0.5, 0.5, 0.5]},
         p0=[1.0, 0.0, 0.0], model_cens="exponential", cens_par=3.0)

⌨️ Command-Line Usage

Install the package and use python -m gen_surv to generate datasets without writing Python code:

python -m gen_surv dataset aft_ln --n 100 > data.csv

🔧 API Overview

genSurvPy/
├── gen_surv/             # Pacote principal
│   ├── __main__.py       # Interface CLI via python -m
│   ├── cphm.py
│   ├── cmm.py
│   ├── tdcm.py
│   ├── thmm.py
│   ├── censoring.py
│   ├── bivariate.py
│   ├── validate.py
│   └── interface.py
├── tests/                # Testes automatizados
│   ├── test_cphm.py
│   ├── test_cmm.py
│   ├── test_tdcm.py
│   ├── test_thmm.py
├── examples/             # Exemplos de uso
│   ├── run_aft.py
│   ├── run_cmm.py
│   ├── run_cphm.py
│   ├── run_tdcm.py
│   └── run_thmm.py
├── docs/                 # Documentação Sphinx
│   ├── source/
│   └── ...
├── scripts/              # Utilidades diversas
│   └── check_version_match.py
├── tasks.py              # Tarefas automatizadas com Invoke
├── TODO.md               # Roadmap de desenvolvimento
├── pyproject.toml        # Configurado com Poetry
├── README.md
├── LICENCE
└── .gitignore

🧠 License

MIT License. See LICENCE for details.

🔖 Release Process

This project uses Git tags to manage releases. A GitHub Actions workflow (version-check.yml) verifies that the version declared in pyproject.toml matches the latest Git tag. If they diverge, the workflow fails and prompts a correction before merging. Run python scripts/check_version_match.py locally before creating a tag to catch issues early.

🌟 Code of Conduct

Please read our Code of Conduct to learn about the expectations for participants in this project.

🤝 Contributing

Please read CONTRIBUTING.md for guidelines on setting up your environment, running tests, and submitting pull requests.

🔧 Development Tasks

Common project commands are defined in tasks.py and can be executed with Invoke:

poetry run inv -l  # list available tasks
poetry run inv test  # run the test suite

📑 Citation

If you use gen_surv in your work, please cite it using the metadata in CITATION.cff. Many reference managers can import this file directly.

Author

Diogo Ribeiro — ESMAD - Instituto Politécnico do Porto

• ORCID: https://orcid.org/0009-0001-2022-7072
• Professional email: dfr@esmad.ipp.pt
• Personal email: diogo.debastos.ribeiro@gmail.com