[R] censboot function for bootstrapping Cox proportional Hazard Model

[GeertSim]

Dear all,

I developed a cox regression model with three independent factors to predict
overall survival in a specific group of patients. I would like to adjust
this model for overoptimism with the censboot function of the boot package.
I would like to use bootstrapping to adjust the regression coefficients of
this model. However, I am unable to complete all the arguments of the
censboot function after searching for several hours. The error I am not able
to fix in the formula is:

> censboot(coxpredictors, mod.coxregr.hub, R=10, sim="ordinary")
Error in censboot(coxpredictors, mod.coxregr.hub, R = 10, sim = "ordinary")
: 
  incorrect number of subscripts on matrix

I assume it has something to do with the strata argument, but I am not sure
how to fix that. Furthermore, is "ordinary" simulation the correct type for
this kind of analysis? I hope someone can help me to complete the formula so
I can perform my bootstrap analysis. You can find my entire script below. 

Many thanks in advance.

Best regards,

Geert Simkens

> library(Hmisc)
> library(survival)
> library(foreign)
> library(boot)
> library(car)
> library(pROC)
> load("~/coxmodel.Rda")
> attach(coxpredictors)
> 
> summary(coxpredictors)
 FollowUpMonths        Event            PCI10              N2          
Symptoms     
 Min.   : 0.1314   Min.   :0.0000   Min.   :0.0000   Min.   :0.000   Min.  
:0.0000  
 1st Qu.:11.3676   1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:0.000   1st
Qu.:1.0000  
 Median :19.6797   Median :0.0000   Median :0.0000   Median :0.000   Median
:1.0000  
 Mean   :23.4967   Mean   :0.4472   Mean   :0.3668   Mean   :0.402   Mean  
:0.8241  
 3rd Qu.:32.2135   3rd Qu.:1.0000   3rd Qu.:1.0000   3rd Qu.:1.000   3rd
Qu.:1.0000  
 Max.   :87.1622   Max.   :1.0000   Max.   :1.0000   Max.   :1.000   Max.  
:1.0000  
> 
> time <- FollowUpMonths
> event <- Event
> X <- cbind(PCI10, N2, Symptoms)
> summary(time)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.1314 11.3700 19.6800 23.5000 32.2100 87.1600 
> 
> # cox regression model with dataname first
> mod.coxregr.hub = function(coxpredictors)
+ {
+     coxph(Surv(time,event == 1) ~ X, method="breslow", model=TRUE)
+ }
> 
> # cox regression model
> coxmodel = coxph(Surv(time,event == 1) ~ X, method="breslow", model=TRUE)
> 
> summary(coxmodel)
Call:
coxph(formula = Surv(time, event == 1) ~ X, model = TRUE, method =
"breslow")

  n= 199, number of events= 89 

            coef exp(coef) se(coef)     z Pr(>|z|)    
XPCI10    1.3179    3.7356   0.2198 5.996 2.02e-09 ***
XN2       0.5587    1.7485   0.2165 2.580  0.00987 ** 
XSymptoms 0.8102    2.2483   0.3787 2.139  0.03241 *  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

          exp(coef) exp(-coef) lower .95 upper .95
XPCI10        3.736     0.2677     2.428     5.747
XN2           1.748     0.5719     1.144     2.673
XSymptoms     2.248     0.4448     1.070     4.723

Concordance= 0.703  (se = 0.033 )
Rsquare= 0.216   (max possible= 0.982 )
Likelihood ratio test= 48.42  on 3 df,   p=1.73e-10
Wald test            = 48.11  on 3 df,   p=2.02e-10
Score (logrank) test = 52.96  on 3 df,   p=1.867e-11
> 
> # bootstrapping formula
> censboot(coxpredictors, mod.coxregr.hub, R=10, sim="ordinary")
Error in censboot(coxpredictors, mod.coxregr.hub, R = 10, sim = "ordinary")
: 
  incorrect number of subscripts on matrix
> 
> 



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