[R] survival probability estimate method

[Peter Jepsen]

Dear John

I am not aware of an R package that does this, but I believe that Patrick Royston's -stpm- function for Stata does. Here's two references found in http://www.stata-journal.com/sjpdf.html?articlenum=st0001_2: 
Royston, P. 2001. Flexible parametric alternatives to the Cox model. Stata Journal 1(1): 1-28.
Royston, P. and M. K. B. Parmar. 2002. Flexible parametric-hazards and proportional odds models for censored survival data, with application to prognostic modelling and estimation of treatment effects. Statistics in Medicine 21: 2175-2197.

Best regards,
Peter.

-----Oprindelig meddelelse-----
Fra: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] På vegne af array chip
Sendt: 4. august 2011 20:45
Til: r-help
Emne: [R] survival probability estimate method

Hi, I was reading a paper published in JCO "Prediction of risk of distant recurrence using 21-gene recurrence score in node-negative and node-positive postmenopausal patients with breast cancer treated with anastrozole or tamoxifen: a TransATAC study" (ICO 2010 28: 1829). The author uses a method to estimate the 9-year risk of distant recurrence as a function of continuous recurrence score (RS). The method is special as author states:
 
"To define the continuous relation between RS, as a linear covariate, and 9-year risk of distant recurrence, the logarithm of the baseline cumulative hazard function was fitted by constrained cubic splines with 3 df. These models tend to be more robust for prediction of survival probabilities and corresponding confidence limits at late follow-up time as a result of the modeling of the baseline cumulative hazard function by natural cubic splines (in contrast to using the crude hazard function itself)."
 
Does R provide a package/function to do this particular method for estimating survival probability as a function of a continuous variable? Is the survest.cph() in rms package doing estimation with just the crude hazard function?
 
Thanks very much!
 
John

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.