R help - Apr 2021 - Contrasts in coxph

I would like to define contrasts on the output of a coxph function. It appears
that the contrast function from the contrast library does not have a method
defined that will allow computation of contrasts on a coxph object.

How does one define and evaluate contrasts for a cox model?

Thank you,
John

John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric
Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)

Dear John,

I googled "contrasts Cox regression" and found

https://stats.stackexchange.com/questions/15603/performing-contrasts-among-treatment-levels-in-survival-analysis

where Frank Harrell reports how to do what you want with his rms 
package. At least I think so, haven't tried it myself.

Best, G?ran

On 2021-04-06 05:28, Sorkin, John wrote:
> I would like to define contrasts on the output of a coxph function.
> It appears that the contrast function from the contrast library does
> not have a method defined that will allow computation of contrasts on
> a coxph object.
> 
> How does one define and evaluate contrasts for a cox model?
> 
> Thank you, John
> 
> John David Sorkin M.D., Ph.D. Professor of Medicine Chief,
> Biostatistics and Informatics University of Maryland School of
> Medicine Division of Gerontology and Geriatric Medicine Baltimore VA
> Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD
> 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone
> number above prior to faxing)
> 
> 
> ______________________________________________ R-help at r-project.org
> mailing list -- To UNSUBSCRIBE and more, see 
> 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.
>

On 4/5/21 8:28 PM, Sorkin, John wrote:
> I would like to define contrasts on the output of a coxph function. It
appears that the contrast function from the contrast library does not have a
method defined that will allow computation of contrasts on a coxph object.
>
> How does one define and evaluate contrasts for a cox model?

I suspect that you are hoping for post-hoc pairwise contrasts. If that's 
the case, then the multcomp package's glht is generally very capable. It 
has three examples in its vignette the involve survivla models. The last 
one constructs a categorical variable for age. That's not a procedure 
that I endorse, but it may have been done for illustration of a method 
and would therefore be free of sin.


library(multcomp)? # console output follows

 > if (require("survival") && require("MASS")) {
+???? ### construct 4 classes of age
+???? Melanoma$Cage <- factor(sapply(Melanoma$age, function(x){if( x <= 
25 ) return(1)
+???????? if( x > 25 & x <= 50 ) return(2)
+???????? if( x > 50 & x <= 75 ) return(3)
+???????? if( x > 75 & x <= 100) return(4) }
+???? ))
+ }
 > summary(Melanoma)
 ????? time????????? status????????? sex age???????????? year??????? 
thickness
 ?Min.?? :? 10?? Min.?? :1.00?? Min.?? :0.0000?? Min.?? : 4.00 Min.?? 
:1962?? Min.?? : 0.10
 ?1st Qu.:1525?? 1st Qu.:1.00?? 1st Qu.:0.0000?? 1st Qu.:42.00 1st 
Qu.:1968?? 1st Qu.: 0.97
 ?Median :2005?? Median :2.00?? Median :0.0000?? Median :54.00 Median 
:1970?? Median : 1.94
 ?Mean?? :2153?? Mean?? :1.79?? Mean?? :0.3854?? Mean?? :52.46 Mean?? 
:1970?? Mean?? : 2.92
 ?3rd Qu.:3042?? 3rd Qu.:2.00?? 3rd Qu.:1.0000?? 3rd Qu.:65.00 3rd 
Qu.:1972?? 3rd Qu.: 3.56
 ?Max.?? :5565?? Max.?? :3.00?? Max.?? :1.0000?? Max.?? :95.00 Max.?? 
:1977?? Max.?? :17.42
 ???? ulcer?????? Cage
 ?Min.?? :0.000?? 1: 14
 ?1st Qu.:0.000?? 2: 73
 ?Median :0.000?? 3:104
 ?Mean?? :0.439?? 4: 14
 ?3rd Qu.:1.000
 ?Max.?? :1.000
 > cm <- coxph(Surv(time, status == 1) ~ Cage, data = Melanoma)
 > ### specify all pair-wise comparisons among levels of "Cage"
 > cm.glht <- glht(cm, mcp(Cage = "Tukey"))
 > cm.glht

 ??? ?General Linear Hypotheses

Multiple Comparisons of Means: Tukey Contrasts


Linear Hypotheses:
 ?????????? Estimate
2 - 1 == 0? -0.2889
3 - 1 == 0?? 0.1910
4 - 1 == 0?? 1.0742
3 - 2 == 0?? 0.4800
4 - 2 == 0?? 1.3631
4 - 3 == 0?? 0.8832


-- 

David.
>
> Thank you,
> John
>
> John David Sorkin M.D., Ph.D.
> Professor of Medicine
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology and
Geriatric Medicine
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.