[R] survival package can't find Ccoxfit6

SeshanV at mskcc.org SeshanV at mskcc.org
Thu Apr 27 18:04:08 CEST 2017

Since my coding philosophy is "why compute something that is not needed" I don't have timing data comparing coxph.fit to the stripped down version. I will try to come up with a test suite.

I do work under Linux (the initial Windows output was because I had both 3.3.1 and 3.4.0 on that machine). So I can get the source code and build the necessary parts into my function/package, but doesn't it defeat the purpose of reusable code?


-----Original Message-----
From: Therneau, Terry M., Ph.D. [mailto:therneau at mayo.edu] 
Sent: Thursday, April 27, 2017 11:41 AM
To: Seshan, Venkatraman E./Epidemiology-Biostatistics; Therneau, Terry M., Ph.D.; r-help
Cc: murdoch.duncan at gmail.com
Subject: Re: survival package can't find Ccoxfit6

On 04/27/2017 09:53 AM, SeshanV at mskcc.org wrote:
> Thank you Drs. Therneau and Murdoch.
> "Why not use coxph.fit?" -- My use case scenario is that I needed the Cox model coefficients for resampled data. I was trying to reduce the computational overhead of coxph.fit (since it will repeated a large number of times) by stripping all the parts that I don't need such as sorting of the data prior to coxfit6.c call and Martingale residual and concordance computations after the parameters are estimated.

That is an interesting use case which I had not thought about.  The first question is just how much slower coxph.fit is than the stripped down version (I'd guess about 1/2 but that is just a guess), and whether that makes a real difference to your code.  If it is spending 10% of its time in the coxph calculation a change to 5% isn't that much, but 90% is something else.  The next is what is the main impediment (I'd guess concordance, but 
again just a guess.)   Perhaps I could add concordance= and/or resid= flags to the fitting 

> Under the R v3.4.0 model one cannot create any modified form of 
> coxph.fit and expect it to work. Worse yet is the following where I 
> copy "coxph.fit" to my workspace as "mycoxph.fit" (works initially 
> because the environment is namespace:survival and fails when 
> environment changed to R_GlobalEnv)

If you were under linux another solution would be to grab the source from github, add your routine to the R/ directory, then R CMD build followed by R CMD INSTALL.  Macintosh is essentially as easy, though you need to install Xcode for the compilers.  The compile toolchain for windows is outside my ken.

Let's keep talking.

Terry T.


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