Formula wrapper for crr from cmprsk
Formula interface for Fine-Gray regression competing risk models.
FGR(formula, data, cause = 1, y = TRUE, ...)
formula |
A formula whose left hand side is a |
data |
A data.frame in which all the variables of |
cause |
The failure type of interest. Defaults to |
y |
logical value: if |
... |
... |
Formula interface for the function crr from the cmprsk
package.
The function crr allows to multiply some covariates by time before
they enter the linear predictor. This can be achieved with the formula
interface, however, the code becomes a little cumbersome. See the examples.
Note that FGR does not allow for delayed entry (left-truncation).
See crr.
Thomas Alexander Gerds tag@biostat.ku.dk
Gerds, TA and Scheike, T and Andersen, PK (2011) Absolute risk regression for competing risks: interpretation, link functions and prediction Research report 11/7. Department of Biostatistics, University of Copenhagen
library(prodlim)
library(survival)
library(cmprsk)
library(lava)
d <- prodlim::SimCompRisk(100)
f1 <- FGR(Hist(time,cause)~X1+X2,data=d)
print(f1)
## crr allows that some covariates are multiplied by
## a function of time (see argument tf of crr)
## by FGR uses the identity matrix
f2 <- FGR(Hist(time,cause)~cov2(X1)+X2,data=d)
print(f2)
## same thing, but more explicit:
f3 <- FGR(Hist(time,cause)~cov2(X1)+cov1(X2),data=d)
print(f3)
## both variables can enter cov2:
f4 <- FGR(Hist(time,cause)~cov2(X1)+cov2(X2),data=d)
print(f4)
## change the function of time
qFun <- function(x){x^2}
noFun <- function(x){x}
sqFun <- function(x){x^0.5}
## multiply X1 by time^2 and X2 by time:
f5 <- FGR(Hist(time,cause)~cov2(X1,tf=qFun)+cov2(X2),data=d)
print(f5)
print(f5$crrFit)
## same results as crr
with(d,crr(ftime=time,
fstatus=cause,
cov2=d[,c("X1","X2")],
tf=function(time){cbind(qFun(time),time)}))
## still same result, but more explicit
f5a <- FGR(Hist(time,cause)~cov2(X1,tf=qFun)+cov2(X2,tf=noFun),data=d)
f5a$crrFit
## multiply X1 by time^2 and X2 by sqrt(time)
f5b <- FGR(Hist(time,cause)~cov2(X1,tf=qFun)+cov2(X2,tf=sqFun),data=d,cause=1)
## additional arguments for crr
f6<- FGR(Hist(time,cause)~X1+X2,data=d, cause=1,gtol=1e-5)
f6
f6a<- FGR(Hist(time,cause)~X1+X2,data=d, cause=1,gtol=0.1)
f6aPlease choose more modern alternatives, such as Google Chrome or Mozilla Firefox.