st: RE: Cox model with a segmented time-dependent covariate

[Kieran McCaul <kieran.mccaul@uwa.edu.au>]

...



Try this:


clear *

input  patient time status treatment age lbr0 t1 lbr1 t2 lbr2 
  1    281   1   1   46    3.2    47 3.8   184    4.9 
  2    604   0   1   57    3.1    94 2.9   187    3.1 
  3    457   1   1   56    2.2    61 2.8    97    2.9 
  4    384   1   1   65    3.9    92 4.7   194    4.9 
  5    341   0   1   73    2.8    87 2.6   192    2.9 
  6    842   1   1   64    2.4    94 2.3   197    2.8 
  7   1514   1   0   69    2.4    74 2.9   202      3 
  8    182   0   0   62    2.4    90 2.5   182    2.9 
  9   1121   1   0   71    2.5   101 2.5   410    2.7 
 10   1411   0   0   69    2.3   182 2.2   847    2.8 
 11    814   1   0   77    3.8   167 3.9   498    4.3 
 12   1071   1   0   58    3.1   108 2.8   187    3.4 
end

gen lbr = lbr0

stset time, f(status) id(patient)

stsplit one, at(1) after(time=t1)
stsplit two, at(1) after(time=t2)

replace lbr = lbr1 if one==1
replace lbr = lbr2 if two==1

list patient time status lbr0 lbr1 lbr2 lbr _st- _t0 , sepby(patient)

stcox lbr treatment age



-----Original Message-----
From: owner-statalist@hsphsun2.harvard.edu [mailto:owner-statalist@hsphsun2.harvard.edu] On Behalf Of Marta Garcia-Granero
Sent: Thursday, 16 January 2014 2:27 AM
To: statalist@hsphsun2.harvard.edu
Subject: st: Cox model with a segmented time-dependent covariate

I am trying to replicate some SPSS commands in Stata. This data were modified from David Collett (2003) Modelling Survival Data in Medical Research (Chapman & Hall/CRC Texts in Statistical Science), and show a hypothetical clinical trial on 12 patients. I want to test if treatment is significant, adjusted for age and ln(bilirrubin). Ln(bilirrubin) were measured 3 times: at baseline (lbr0); approximately at 3 months -with the exact day recorded in t1 (lbr1); and approximately at 6 months - with exact day recorded in t2 (lbr2).

+----------------------------------------------------------------------------+
      | patient   time   status   treatment   age   lbr0    t1 lbr1    
t2   lbr2 |
|----------------------------------------------------------------------------|
   1. |       1    281     Died     Placebo    46    3.2    47 3.8   
184    4.9 |
   2. |       2    604    Alive     Placebo    57    3.1    94 2.9   
187    3.1 |
   3. |       3    457     Died     Placebo    56    2.2    61 2.8    
97    2.9 |
   4. |       4    384     Died     Placebo    65    3.9    92 4.7   
194    4.9 |
   5. |       5    341    Alive     Placebo    73    2.8    87 2.6   
192    2.9 |
|----------------------------------------------------------------------------|
   6. |       6    842     Died     Placebo    64    2.4    94 2.3   
197    2.8 |
   7. |       7   1514     Died   Treatment    69    2.4    74 2.9   
202      3 |
   8. |       8    182    Alive   Treatment    62    2.4    90 2.5   
182    2.9 |
   9. |       9   1121     Died   Treatment    71    2.5   101 2.5   
410    2.7 |
  10. |      10   1411    Alive   Treatment    69    2.3   182 2.2   
847    2.8 |
|----------------------------------------------------------------------------|
  11. |      11    814     Died   Treatment    77    3.8   167 3.9   
498    4.3 |
  12. |      12   1071     Died   Treatment    58    3.1   108 2.8   
187    3.4 |
+----------------------------------------------------------------------------+

With SPSS, I had to define a time varying covariate (T_COV_) and add it to the model:

TIME PROGRAM.
COMPUTE T_COV_ = (T_<t1)*lbr0 + (T_>=t1&T_<t2)*lbr1 + (T_>=t2)*lbr2.
COXREG   time
   /STATUS=status(1)
   /CONTRAST (treatment)=Indicator
   /METHOD=ENTER T_COV_ treatment age.

In SPSS, T_ is the same as Stata's _t.

This is the output:
                      coef      se         HR    ----95%CI------ 
LR        de     sig
T_COV_       4.533    2.488    93.05    0.71    12192.54 10.865    1    
0.001
Treatment    4.749    2.860    115.50    0.42    31421.66 5.814    1    
0.016
Age            -0.078     0.094    0.93     0.77    1.11    0.808 1    0.369

With Stata, I suspect I have to use, somehow, -stsplit- and -stjoin- , but I can't figure how (even though I have used help stsplit, and read the whole PDF on stcox).

Any hints?

Thanks,
Marta Garcia-Granero

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