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

[sdzhangping]

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)~bmt+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)  

      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