[R] cumulative incidence for mstate in Survival package in R

[Terry Therneau]

Question 1: How to get just 2 cumulative incidence curves when there are multiple covariates.
   I don't understand what you want.  Assume that we have "liver transplant" and "death 
while waiting for a transplant" as my two events.  There are overall curves (2), or one 
can create curves separately for each sex, or for different institutions.  What do you 
mean by "a curve for age"?
   If you want competing risks after Cox model adjustment, see the mstate package.

Question 2: "mine" data.  There is no such data.  This was a hypthetical example in the 
document, and I chose a poor name for the data set; "your_data_set" would have been 
better.  I was using "mine" in the sense of "this data set is mine, it belongs to me", and 
now see that it could confuse someone.  The file sourcecode.pdf is intended to document 
the computational algorithms, but not how a user would approach the function.  A vignette 
is planned, someday...

Terry Therneau


On 12/30/2013 04:04 PM, Jieyue Li wrote:
> Dear All,
>
> I want to have the cumulative incidence curves for 'mstate' data using Survival package in
> R. But I got some problems:
> I. Problem 1:
> 1. If I only use intercept without any covariates, I can have 'right' cumulative incidence
> curves (2 for 2 competing risks):
> library(Survival)
> fitCI <- survfit(Surv(stop, status*as.numeric(event), type="mstate") ~ 1,data=mgus1,
> subset=(start==0))
> plot(fitCI)
> 2. If I include one variate ('sex'), I get 4 curves (attached; I guess because there are
> two levels in 'sex' and 2 competing risks):
> fitCI <- survfit(Surv(stop, status*as.numeric(event), type="mstate") ~sex,data=mgus1,
> subset=(start==0))
> plot(fitCI)
> However, I want to just have 2 cumulative incidence curves estimated from several
> covariates (such as 'sex', 'age', 'alb', etc. in mgus1). Could you please help me to do
> that? Thank you very much!
> II. Problem 2:
> I try using an example from sourcecode.pdf:
> fit <- survfit(Surv(time, status, type=’mstate’) ~ sex, data=mine)
> but where can I have the 'mine' data? Thank you!
>
> Best,
>
> Jieyue
>