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A survival analysis interface for Julia

Home Page: https://raphaels1.github.io/SurvivalAnalysis.jl

License: MIT License

Julia 100.00%

julia survival-analysis time-to-event

survivalanalysis.jl's Introduction

SurvivalAnalysis.jl: A survival analysis interface for Julia

Status	Testing	Coverage	Docs	Codebase

About

Survival analysis interface in Julia, still very experimental. Tries to build on my R experience with mlr3proba and distr6.

Related Packages

JuliaStats/Survival.jl implements right-censored time-to-event types, Cox PH, Kaplan-Meier and Nelson-Aalen estimators. Last commit 2022.
Testispuncher/Survival.jl implements non-parametric estimators and some plots. Last commit 2017.
kkholst/EventHistory.jl implements different censoring and truncation types and Cox PH. Last commit 2018.

Features

Current

Kaplan Meier estimator (+plotting)
Nelson Aalen estimator (+plotting)
Parametric PH models (Exponential and Weibull)
Parametric AFT models (Exponential and Weibull)
Discrete and continuous survival prediction objects, including distribution, linear predictor and general risk return types
Plotting for non parametric estimators
Surv object for unified censoring indicator (functionality for left, right, interval)
Extended formula interface for survival objects
Log-rank tests

Planned

Contributors

_{Raphael Sonabend}
🐛 💻 🖋 📖 🎨 💡 🤔 🚧 📆 💬 🔬 👀

⚠️

✅

_{Kerby Shedden}
📖 💻

_{Moritz Schauer}
👀

survivalanalysis.jl's People

Contributors

Stargazers

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kshedden jdalbers nilshg

survivalanalysis.jl's Issues

Add ImproperDistribution <: DiscreteNonParametric

Find out why var_cov < 0 for parametric models]

    ## FIXME - NEED TO FIGURE OUT WHY VAR_COV SOMETIMES < 0

https://github.com/RaphaelS1/Survival.jl/blob/ca1a424f366730863a28f06fd62f5742f021b65e/src/ParametricSurvival.jl#L40

Add issues templates

Add residuals (Schoenfeld, etc.)

Combined files by inheritance

https://github.com/RaphaelS1/SurvivalAnalysis.jl/blob/11cbc982e6a5b2df2469685613106a674786b542/src/ContinuousPHDistribution.jl#L1

e.g. put ContinuousPHDistr and ContinuousAFTDistr into ContinousUnivariateDistribution.jl

Add tutorials

https://diataxis.fr/

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Add explanations

https://diataxis.fr/

Find out why var_cov < 0 for parametric models

    ## FIXME - NEED TO FIGURE OUT WHY VAR_COV SOMETIMES < 0

https://github.com/RaphaelS1/Survival.jl/blob/ca1a424f366730863a28f06fd62f5742f021b65e/src/ParametricSurvival.jl#L40

mlr3proba integration

Add Root Mean Squared Error

Add scoring rules

(and standardised)

diataxis documentation

https://diataxis.fr/

Update index.md (can copy README)
Add a brief document on diataxis (include their fig) and how to use our documentation
Update examples.md

Tutorials

Add tutorial placeholder + open issue

How-to guides

Add how-to placeholder + open issue

Reference

Restructure auto API as needed
Update README
Document structs/classes
Document methods

Explanation

Add explanation placeholder + open issue

Strings -> Symbols in arguments (where sensible)

https://discourse.julialang.org/t/when-should-a-function-accept-a-symbol-as-an-argument/43510/35

Add how-to guides

https://diataxis.fr/

Add measure dispatch on Prediction objects

Add PO models

Manually sort docs

Improve printed structure outputs (e.g. Kaplan-Meier)

Add calibration measures

Add contributorguidelines.md

Add Mean Absolute Error

Add Bayesian interface to Turing.jl

Test all-contributors

Change type tests to === for better efficiency

https://github.com/RaphaelS1/SurvivalAnalysis.jl/blob/11cbc982e6a5b2df2469685613106a674786b542/src/ParametricPH.jl#L40

Remove unicode publicly everywhere

https://github.com/RaphaelS1/SurvivalAnalysis.jl/blob/11cbc982e6a5b2df2469685613106a674786b542/src/ContinuousPHDistribution.jl#L2

Add KM and NA support for more censoring types

Add code of conduct

Add generic plotting recipes

Improve analytical optimisation throughout

Add more parametric families for AFT

How should the package be structured?

#62

Add stratified KM and NA support

Add discrimination measures

Add long-rank, MH, etc. tests

Add methods to calculate hazard ratios from PH models (and add to show)

Add CoxPH

Move test specific dependencies to Test/Project.toml

Debug stochastic failure in doctest

https://github.com/RaphaelS1/SurvivalAnalysis.jl/runs/8171250046?check_suite_focus=true#step:5:10

Add PR templates

Add survival time measures

Add c-index measures

Copy from https://mlr3proba.mlr-org.com/reference/mlr_measures_surv.cindex.html

MLJ integration

Dead link in README.md

The link to docs-stable is dead.
https://raphaels1.github.io/SurvivalAnalysis.jl/stable

Add predict type transformations

Fairness.jl

https://discourse.julialang.org/t/ann-survivalanalysis-jl/86680/4?u=raphaels1

Add Mean Squared Error

Unify variable names everywhere: surv/survival, distr/distribution

https://github.com/RaphaelS1/Survival.jl/blob/ca1a424f366730863a28f06fd62f5742f021b65e/test/test_survival_estimators.jl#L56

Fix inversion issue in parametric survival models

https://github.com/RaphaelS1/Survival.jl/blob/ca1a424f366730863a28f06fd62f5742f021b65e/src/ParametricSurvival.jl#L30

Add R2 measures

Nagelk
O'Quigley
Xu

vollmersj / survivalanalysis.jl Goto Github PK

survivalanalysis.jl's Introduction

SurvivalAnalysis.jl: A survival analysis interface for Julia

About

Related Packages

Features

Current

Planned

Contributors

survivalanalysis.jl's People

Contributors

Stargazers

Watchers

Forkers

survivalanalysis.jl's Issues

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