Skip to content

censboot function for bootstrapping Cox proportional Hazard Model

2 messages · GeertSim, David Winsemius

#
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:
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
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
Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.1314 11.3700 19.6800 23.5000 32.2100 87.1600
+ {
+     coxph(Surv(time,event == 1) ~ X, method="breslow", model=TRUE)
+ }
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
Error in censboot(coxpredictors, mod.coxregr.hub, R = 10, sim = "ordinary")
: 
  incorrect number of subscripts on matrix
--
View this message in context: http://r.789695.n4.nabble.com/censboot-function-for-bootstrapping-Cox-proportional-Hazard-Model-tp4707989.html
Sent from the R help mailing list archive at Nabble.com.
#
On May 31, 2015, at 2:10 PM, GeertSim wrote:

            
My guess (and one can only guess since there is no way to see the data) is that it has to do with attaching that dataframe and supplying arguments to the function (for instance 'event' and 'time` that are outside the evaluation environment that is expected inside the boot function. Using `attach` is generally unsafe and not appropriate for arguments passed into regression functions, especially so for boot-functions. More guesswork: I suspect that most of R-Core would rather that it did not exist.