[R] survival data with competing risks and time-dependent covariates!

[David Winsemius]

Are you sure you are using coxphf correctly for this purpose. Since  
you have not identified what package your function comes from, it's  
not possible for me to check the appropriate help page, but had you  
been using the coxph function in the survival package, you would have  
been using the cluster() formulation to group your individuals. At the  
moment I do not see that you are passing the id variable to the  
function in any manner.

-- 
David Winsemius, MD

On Mar 26, 2010, at 1:27 AM, sdzhangping wrote:

> Dear friends:
>
>  I’m very interested in the analysis of survival data of leukemic  
> patients, which involves competing risks and time-dependent  
> covariates (infections or relapse of leukemia after BMT). In my  
> present work, I’d like to estimate the risk of chemotherapy, BMT or  
> gvhd on the onset and prognosis of invasive fungal infections (IFI).  
> In detail, the leukemic patients will receive several cycles of  
> chemotherapy and some of them will receive BMT. The patients have  
> three outcomes, that’s acquisition of IFI, death free from IFI or  
> IFI free survival. My puzzle is:
>
> (1)Dose multi-state model fit this situation?
>
> (2)I tried to fit coxphf model:  fit =  
> coxphf(Surv(start,stop,ifi==1)~bmt, data=ifi). The system always  
> goes wrong when variable “gvhd” was fitted.  
> [coxphf(Surv(start,stop,ifi==1)~gvhd, data=ifi)]. Is there something  
> wrong with my data format?
>
> Thank you!
>
> Ping Zhang
>
> Mar 26 2010
>
>
>
> simulation dataset of six patients: (with ifi.csv in the attachment)

No attachment. Is it possible that you have not read the Posting Guide  
as thoroughly as you should have?

>
>      id  start stop ifi chemo  bmt  gvhd  death
>
>       1     0     7   0        1      0      0       0     #chemo at  
> d7 and died at d30
>
>       1     0     7   0        1      0      0       0
>
>       2     0     8   0        1      0      0        0    #chemo1  
> at d7, ifi at d100, chemo2 at d120 ,bmt at d200 and death at d450
>
>       2    8     100  1      0       0     0        0
>
>       2    100  120  0      1       0     0       0
>
>       2    120  200  0     0       1      0        0
>
>       2    200   450  0    0       0      0        1
>
>       3    0         6   0     1      0      0        0   #chemo1 at  
> d6, ifi at d44, chemo2 at d60, censor at d300
>
>       3    6        44  1     0      0       0       0
>
>       3    44       60  0     1      0      0       0
>
>       3    60     300  0      0      0      0       0
>
>       4      0       10  0      1      0      0       0        
> #chemo1 at d10, chemo2 at d60,
>
>       4     10      60   0     1      0      0       0       #bmt at  
> d120, censor at d300
>
>       4     60      120  0     0     1      0       0
>
>       4     120     300  0    0     0      0        0
>
>       5        0       9    1     0    0       0       0       #ifi  
> at d9, die at d30
>
>       5        9       30  0     0     0       0       0
>
>       6      300     301  0     0     1       0      0      #(left  
> censored) bmt at d301, gvhd at d330, ifi at 340, death at 350
>
>       6      301     330  0     0     0       1      0
>
>       6      330     340  1     0      0      0      0
>
>       6      340     350  0     0     0       0      1
>
>
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.