Welcome to lifelines Discussions!

[CamDavidsonPilon]

👋 Welcome!

Hi there! I'm Cameron, the maintainer of lifelines. I'd like to try this forum out for support and questions on lifelines (previously I suggested Gitter, but I'd like to try something new).

Please start a new "discussion" instead of posting here!

[memolinda]

Hi, I am really new on survival analysis and in particular on lifelines. I am trying to plot the effect of varying a covariate by keeping all the rest constant as in the example: https://lifelines.readthedocs.io/en/latest/Survival%20Regression.html#cox-s-proportional-hazard-model by using CoxPHFitter function. Now, where I can find the documentation about the plot_partial_effects_on_outcome. I can't find anywhere (but maybe I didn't search correctly). I would like to now which parameters to pass and in particular the meaning of value. Thanks

[CamDavidsonPilon]

Hi @memolinda, you're right - the docs are hidden on this (I've made an issue to fix). Here are some examples though: https://lifelines.readthedocs.io/en/latest/Survival%20Regression.html#plotting-the-effect-of-varying-a-covariate

The important parameters to pass are covariates, which is a string (or list of strings) to signal which covariates we wish to vary (and all else keep constant). Also important is values, which tells the function which values the covariate should take on.

[BenRossJenkins]

Hi @CamDavidsonPilon, I am a big fan of lifelines. I was wondering if there is any way to make the plots interactive? This would be very useful when there are a number of different survival curves plotted. Also, how do you best compare the survival curves with a large difference in the number of samples? Thank you.

[CamDavidsonPilon]

Hi @BenRossJenkins - there's no native way to make the plots interactive, you'd have to export the data and plot it in Altair, or Bokeh, etc. Maybe even streamlit to make it web-based?

how do you best compare the survival curves with a large difference in the number of samples

Exactly how do you want to compare them? Like, do you want to know if there are different overall? Or different at a specific time point? With large number of samples, most statistical tests will come back rejecting the null, so I don't know how much one can learn from a statistical test.

[gunesevitan]

Hello, I'm very new to survival analysis. What are the proper ways of evaluating generalizability of Kaplan Meier and Cox Proportional Hazard models on unseen test sets? I noticed those estimators have no predict functionality, so how should I properly calibrate model outputs into probabilities on time axis for every subject?

[CamDavidsonPilon]

Hi @gunesevitan - please start a new "discussion" at this link: https://github.com/CamDavidsonPilon/lifelines/discussions

[brunnerpascal]

I just wanted to say thank you for this beautiful library and awesome documentation!!