Dear R users,
I d like to assess the effect of "treatment" covariate on a disease relapse
risk with the package cmprsk.
However, the effect of this covariate on survival is time-dependent
(assessed with cox.zph): no significant effect during the first year of
follow-up,
then after 1 year a favorable effect is observed on survival (step
function might be the correct way to say that ?).
For overall survival analysis
I have used a time dependent Cox model which has confirmed this positive effect
after
1 year.
Now I m moving to disease relapse incidence and a similar time dependency seems
to be present.
what I d like to have is that: for
patients without "treatment" the code for "treatment" covariate is
always 0, and for patients who received "treatment" covariate I d like
to have it = 0 during time interval 0 to 1 year, and equal to 1 after 1
year. Correct me if I m wrong in trying to do so.
First, I have run the following script (R2.7.1 under XPpro) according to
previous advices:
library(cmprsk)
attach(LAMrelapse)
fit1<- crr(rel.t, rel.s, treatment, treatment, function(uft)
cbind(ifelse(uft<=1,1,0),ifelse(uft>1,1,0)), failcode=1,
cencode=0, na.action=na.omit, gtol-06, maxiter)
fit1
where:
rel.t = time to event (in years)
rel.s = status , =1 if disease relapse, =2 if death from non disease
related cause (toxicity of previous chemotherapy), =0 if alive &
not in relapse
treatment =
binary covariate (value: 0 or 1) representing the treatment to test
(different from chemotherapy above, with no known toxicity)
I have not yet added other covariates in the model.
this script gave me the following result:
> fit1 <- crr(relcmp.t, relcmp.s, treatment, treatment, function(uft)
> cbind(ifelse(uft <= 1, 1, 0), ifelse(uft > 1, 1, 0)), failcode = 1, cencode =
> 0,
na.action = na.omit, gtol = 1e-006, maxiter = 10)
> fit1
convergence: TRUE
coefficients:
[1] -0.6808 0.7508
standard errors:
[1] 0.2881 0.3644
two-sided p-values:
[1] 0.018 0.039
...That I dont understand at all since it looks like if "treatment"
covariate had also a significant effect of the first period of time !?
This is absolutely not the case.
So I m surely wrong with a part of this script... cov2 and tf are
pretty obscure for me in the help file of the package. I would really
appreciate advices regarding these 2 "terms".
I was thinking that I might changed : cbind(ifelse(uft <= 1, 1, 0), ifelse(uft
> 1, 1, 0) into: cbind(ifelse(uft <= 1, 0, 1),
ifelse(uft > 1, 1, 0)
But since I only have one covariate (treatment) to test, shouldnt I only write
the following:
fit1<- crr(rel.t,
rel.s, treatment, treatment, function(uft) ifelse(uft<=1,0,1)), failcode=1,
cencode=0, na.action=na.omit, gtol-06, maxiter)
which gives me :
> fit1
convergence: TRUE
coefficients:
[1] 0.06995 -0.75080
standard errors:
[1] 0.2236 0.3644
two-sided p-values:
[1] 0.750 0.039
which, if I understand things
correctly (I m not sure at all !) confirms that before 1 year, the effect of
"treatment" covariate is not
significant, but is significant after 1 year of follow up. But there I m again
not sure of the result I obtain...
any help would be greatly appreciated with cov2 and tf
thanks for if you have some time for this,
Philippe Guardiola
_____________________________________________________________________________
o.fr
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