https://github.com/vollmersj/survivalanalysis.jl

A survival analysis interface for Julia
https://github.com/vollmersj/survivalanalysis.jl

julia survival-analysis time-to-event

Last synced: 5 days ago
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A survival analysis interface for Julia

• Host: GitHub
• URL: https://github.com/vollmersj/survivalanalysis.jl
• Owner: vollmersj
• License: mit
• Created: 2022-06-18T21:41:17.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2023-02-08T03:59:13.000Z (over 2 years ago)
• Last Synced: 2024-11-12T13:02:27.214Z (6 months ago)
• Topics: julia, survival-analysis, time-to-event
• Language: Julia
• Homepage: https://raphaels1.github.io/SurvivalAnalysis.jl
• Size: 558 KB
• Stars: 31
• Watchers: 4
• Forks: 3
• Open Issues: 30
• Metadata Files:
  • Readme: README.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: .github/CODE_OF_CONDUCT.md

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README

        
# SurvivalAnalysis.jl: A survival analysis interface for Julia

| Status | Testing | Coverage | Docs | Codebase |

| -------| ------- | -------- | ---- | ----- |

| [![deps](https://juliahub.com/docs/SurvivalAnalysis/deps.svg)](https://juliahub.com/ui/Packages/SurvivalAnalysis/N9zkY?t=2) 
 [![version](https://juliahub.com/docs/SurvivalAnalysis/version.svg)](https://juliahub.com/ui/Packages/SurvivalAnalysis/N9zkY) 
 [![pkgeval](https://juliahub.com/docs/SurvivalAnalysis/pkgeval.svg)](https://juliahub.com/ui/Packages/SurvivalAnalysis/N9zkY) | [![CI](https://github.com/RaphaelS1/SurvivalAnalysis.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/RaphaelS1/SurvivalAnalysis.jl/actions/workflows/CI.yml) | [![codecov](https://codecov.io/gh/RaphaelS1/SurvivalAnalysis.jl/branch/main/graph/badge.svg?token=R1QK5X4RVP)](https://codecov.io/gh/RaphaelS1/SurvivalAnalysis.jl) | [![](https://img.shields.io/badge/docs-stable-darkblue.svg)](https://raphaels1.github.io/SurvivalAnalysis.jl/stable) 
 [![](https://img.shields.io/badge/docs-dev-lightblue.svg)](https://raphaels1.github.io/SurvivalAnalysis.jl/dev) | [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/RaphaelS1/SurvivalAnalysis.jl/blob/main/code_style_blue.md) 
 ![Experimental](https://lifecycle.r-lib.org/articles/figures/lifecycle-experimental.svg) 
 [![MIT](https://img.shields.io/badge/License-MIT-yelllow)](https://opensource.org/licenses/MIT) |

## About

Survival analysis interface in Julia, still very experimental. Tries to build on my R experience with [mlr3proba](https://github.com/mlr-org/mlr3proba) and [distr6](https://github.com/alan-turing-institute/distr6).

## Related Packages

* [JuliaStats/Survival.jl](https://github.com/JuliaStats/Survival.jl) implements right-censored time-to-event types, Cox PH, Kaplan-Meier and Nelson-Aalen estimators. Last commit 2022.

* [Testispuncher/Survival.jl](https://github.com/Testispuncher/Survival.jl) implements non-parametric estimators and some plots. Last commit 2017.

* [kkholst/EventHistory.jl](https://github.com/kkholst/EventHistory.jl) implements different censoring and truncation types and Cox PH. Last commit 2018.

## Features

### Current

* [x] Kaplan Meier estimator (+plotting)

* [x] Nelson Aalen estimator (+plotting)

* [x] Parametric PH models (Exponential and Weibull)

* [x] Parametric AFT models (Exponential and Weibull)

* [x] Discrete and continuous survival prediction objects, including distribution, linear predictor and general risk return types

* [x] Plotting for non parametric estimators

* [x] Surv object for unified censoring indicator (functionality for left, right, interval)

* [x] Extended formula interface for survival objects

* [x] [Log-rank tests](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/10)

### Planned

* [ ] [CoxPH](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/8)

* [ ] [Residuals (Schoenfeld etc.)](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/11)

* [ ] [Predict type transformations](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/12)

* [ ] [Generic plotting functionality](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/13)

* [ ] [Proportional odds functionality](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/14)

* [ ] [More parametric AFTS](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/15)

* [ ] [Analytical optimisation](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/16)

* [ ] [Discrimination measures](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/17)

* [ ] [Scoring rules](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/19)

* [ ] [Calibration measures](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/18)

* [ ] [Bayesian interface](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/20)

* [ ] [mlr3proba integration](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/21)

* [ ] [MLJ integration](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/22)

* [ ] [Documentation](https://github.com/RaphaelS1/SurvivalAnalysis.jl/issues/9)

## Contributors

[![All Contributors](https://img.shields.io/badge/all_contributors-3-orange.svg?style=flat-square)](#contributors-)

  

    

      
Raphael Sonabend
🐛 💻 🖋 📖 🎨 💡 🤔 🚧 📆 💬 🔬 👀 ⚠️ ✅

      
Kerby Shedden
📖 💻

      
Moritz Schauer
👀