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IndexError during compute_residuals

See original GitHub issue

Hi Cam,

I successfully fitted a survival regression (CoxPHFitter) on my data. However, I cannot compute the shoenfeld (_compute_schoenfeld called by residuals = self.compute_residuals(training_df, kind="scaled_schoenfeld")) and get the following error:

df = pd.DataFrame(schoenfeld_residuals[E, :], columns=self.hazards_.columns, index=index[E])
IndexError: boolean index did not match indexed array along dimension 0; dimension is 3654 but corresponding boolean dimension is 3743

The error come from schoenfeld_residuals[E, :] with schoenfeld_residuals of shape (3654, 6) and E (3743,).

I guess E correspond to the event and this a censorship issue?

This seems related to this issue.

By the way, thank you very much for lifelines–I didn’t know much on survival analysis and was ready in no time thank to the clear api and docs.

Issue Analytics

State:
Created 5 years ago
Reactions:1
Comments:5 (4 by maintainers)

Top GitHub Comments

1reaction

CamDavidsonPiloncommented, Jan 24, 2019

AFAIK, this is fixed

0reactions

romainmartinezcommented, Jan 25, 2019

Everything is working fine with the fix, thanks!

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