I’m reading your tutorial vignette for the mstate package, https://cran.r-project.org/web/packages/mstate/vignettes/Tutorial.pdf, and found a statement which seems inconsistent with the data / R output. On page 9, you write:
There is no evidence of non-proportionality of the baseline transition intensities of transitions 2 (p=0.496 for pr).
However, the table for cox.zph(c2) above clearly does show evidence of non-proportionality. The p-value is listed as 5.2e-05 (i.e., 0.000052), not 0.496. I have also tried running the corresponding code with the latest version of R and the packages, and I too get a p-value of 5.2e-05.
(On the other hand, based on the figure in the vignette and in the original tutorial, proportional hazards does seem like a reasonable assumption, so I’m not sure what’s going on.)
I’m reading your tutorial vignette for the mstate package, https://cran.r-project.org/web/packages/mstate/vignettes/Tutorial.pdf, and found a statement which seems inconsistent with the data / R output. On page 9, you write:
However, the table for
cox.zph(c2)above clearly does show evidence of non-proportionality. The p-value is listed as 5.2e-05 (i.e., 0.000052), not 0.496. I have also tried running the corresponding code with the latest version of R and the packages, and I too get a p-value of 5.2e-05.(On the other hand, based on the figure in the vignette and in the original tutorial, proportional hazards does seem like a reasonable assumption, so I’m not sure what’s going on.)