Survival analysis in Julia


#1

Hi all,
What are good packages for survival analysis in Julia (i.e. working with truncated data, Kaplan-Meier estimator, Cox model and so on…)? So far I only found packages that seemed incomplete/abandoned (e.g.[https://github.com/ContaTP/Survival.jl] (https://github.com/ContaTP/Survival.jl)) or this unmerged PR in GLMnet.
I wanted to know if I’m missing something and if/where this set of analysis will become part of Julia Statistics ecosystem.

Thanks,
Pietro


#2

There’s also https://github.com/kkholst/EventHistory.jl. But none of the packages appear to be under very active development. As often with free software, it will depend on whether somebody steps in or not…


#3

If you need a stop-gap measure, you can call into Python or R. But the best solution may be to write your own package, as @nalimilan suggests.


#4

I was just wondering the same thing. I am taking survival analysis this semester. Looks like I will have to lean on R. https://www.openintro.org/download.php?file=survival_analysis_in_R&referrer


#5

In the end I started working on it, although very slowly as I don’t have as much time as I’d like to dedicate to this project. Out of curiosity, what type of analysis would you need? Here’s a list of what I’m planning to implement:

  • Kaplan-Meier estimate of the survival function
  • Nelson-Aalen estimate of the cumulative hazard
  • Some smoothing to get hazard from cumulative hazard
  • Cox proportional hazard models
  • Accelerated failure time models

Feel free to let me know if there are more things you’d like to see implemented/implement yourself.


#6

It is hard for me to know. I am just doing a grad level class - no research. If you are willing I would love to contribute. Let me know what you need.


#7

Cool! I’ll try to work a bit more on the core structure of the thing and, as soon as the “skeleton” is clear I’ll open an issue with a “to do list”.