sdzhangping
2010-Mar-26 05:01 UTC
[R] survival data with competing risks and time-dependent covariates!
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: id start stop ifi chemo bmt gvhd death 1 0 7 0 1 0 0 0 #chemo at d7 and died at d30 1 7 30 2 0 0 0 1 2 0 8 0 1 0 0 0 #chemo1 at d7, ifi at d100, chemo2 at 2 8 100 1 0 0 0 0 # d120, bmt at d200 and die at d450 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, 3 6 44 1 0 0 0 0 # censor at d300 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 1 6 300 301 0 0 1 0 0 #(left censorsed) bmt at d300, gvhd at 6 301 330 0 0 0 1 0 #330, ifi at d340, die at d350 6 330 340 1 0 0 0 0 6 340 350 0 0 0 0 1
sdzhangping
2010-Mar-26 05:27 UTC
[R] survival data with competing risks and time-dependent covariates!
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)
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
sdzhangping
2010-Mar-28 13:08 UTC
[R] survival data with competing risks and time-dependent covariates!
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
Stefan Grosse
2010-Mar-28 13:41 UTC
[R] survival data with competing risks and time-dependent covariates!
Am 28.03.2010 15:08, schrieb sdzhangping:> 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? > ted, minimal, self-contained, reproducible code. >You were posting exactly this question already on Friday twice and then today twice. You have been pointed out that you might be using the wrong function. So why should anyone answer you question when you do not show any effort? You did not even ask back. Stefan