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Supplemental information for ‘Tutorial on survival modeling with applications to omics data ’

This is a supplement for the article ‘Tutorial on survival modeling with application to omics data’, see the step-by-step R tutorial here.

Citation

Zhao, Z., Zobolas, J., Zucknick, M., & Aittokallio, T. (2024). Tutorial on survival modeling with applications to omics data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btae132

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fix measure terminology

RCLL is an overall predictive accuracy measure and not a calibration measure

Use https://doi.org/10.1186/S12874-017-0336-2 this paper for reference and Raphael's thesis

Change "The following code shows that the nonlinear part of the smoothing spline does not have a significant effect (p=0.00013)" to "The following code shows that the nonlinear part of the smoothing spline has a significant effect (p=0.00013)".

Notice: mlr3extralearners version is important (it is not a bug)

Hi all,
Thanks a lot for this great tutorial, this tutorial has taught me a lot.

When I learned this textbook step by step, a weird result appeared in section "Model evaluation (mlr3)". where I cannot get "the survival distribution predictions (distr) along with the linear predictors (lp)".

After careful examination, I found that the release version of mlr3extralearners does not meet the requirements of this tutorial. . Instead, it is necessary to use its development version(mlr3extralearners_0.7.1-9000). The development version has added many features that are not available in the release version, including "survival distribution predictions".

May this help others.

Once again, thank you for this outstanding work. Have a nice day :)