[R] survival probability estimate method

[array chip]

Dear Peter,

Thanks very much for the references. It seems the method is based on parametric proportional hazard models by incorporating cubic spline of the baseline hazards, not sure if tweaking survreg() would do?

Best,

John


----- Original Message -----
From: Peter Jepsen <PJ at DCE.AU.DK>
To: 'array chip' <arrayprofile at yahoo.com>; r-help <r-help at r-project.org>
Cc: 
Sent: Thursday, August 4, 2011 1:09 PM
Subject: SV: [R] survival probability estimate method

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

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