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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/eventTime.R
\name{eventTime}
\alias{eventTime}
\alias{eventTime<-}
\title{Add an observed event time outcome to a latent variable model.}
\usage{
eventTime(object, formula, eventName = "status", ...)
}
\arguments{
\item{object}{Model object}
\item{formula}{Formula (see details)}
\item{eventName}{Event names}
\item{\dots}{Additional arguments to lower levels functions}
}
\description{
For example, if the model 'm' includes latent event time variables
are called 'T1' and 'T2' and 'C' is the end of follow-up (right censored),
then one can specify
}
\details{
\code{eventTime(object=m,formula=ObsTime~min(T1=a,T2=b,C=0,"ObsEvent"))}
when data are simulated from the model
one gets 2 new columns:
- "ObsTime": the smallest of T1, T2 and C
- "ObsEvent": 'a' if T1 is smallest, 'b' if T2 is smallest and '0' if C is smallest
Note that "ObsEvent" and "ObsTime" are names specified by the user.
}
\examples{
# Right censored survival data without covariates
m0 <- lvm()
distribution(m0,"eventtime") <- coxWeibull.lvm(scale=1/100,shape=2)
distribution(m0,"censtime") <- coxExponential.lvm(rate=1/10)
m0 <- eventTime(m0,time~min(eventtime=1,censtime=0),"status")
sim(m0,10)
# Alternative specification of the right censored survival outcome
## eventTime(m,"Status") <- ~min(eventtime=1,censtime=0)
# Cox regression:
# lava implements two different parametrizations of the same
# Weibull regression model. The first specifies
# the effects of covariates as proportional hazard ratios
# and works as follows:
m <- lvm()
distribution(m,"eventtime") <- coxWeibull.lvm(scale=1/100,shape=2)
distribution(m,"censtime") <- coxWeibull.lvm(scale=1/100,shape=2)
m <- eventTime(m,time~min(eventtime=1,censtime=0),"status")
distribution(m,"sex") <- binomial.lvm(p=0.4)
distribution(m,"sbp") <- normal.lvm(mean=120,sd=20)
regression(m,from="sex",to="eventtime") <- 0.4
regression(m,from="sbp",to="eventtime") <- -0.01
sim(m,6)
# The parameters can be recovered using a Cox regression
# routine or a Weibull regression model. E.g.,
\dontrun{
set.seed(18)
d <- sim(m,1000)
library(survival)
coxph(Surv(time,status)~sex+sbp,data=d)
sr <- survreg(Surv(time,status)~sex+sbp,data=d)
library(SurvRegCensCov)
ConvertWeibull(sr)
}
# The second parametrization is an accelerated failure time
# regression model and uses the function weibull.lvm instead
# of coxWeibull.lvm to specify the event time distributions.
# Here is an example:
ma <- lvm()
distribution(ma,"eventtime") <- weibull.lvm(scale=3,shape=1/0.7)
distribution(ma,"censtime") <- weibull.lvm(scale=2,shape=1/0.7)
ma <- eventTime(ma,time~min(eventtime=1,censtime=0),"status")
distribution(ma,"sex") <- binomial.lvm(p=0.4)
distribution(ma,"sbp") <- normal.lvm(mean=120,sd=20)
regression(ma,from="sex",to="eventtime") <- 0.7
regression(ma,from="sbp",to="eventtime") <- -0.008
set.seed(17)
sim(ma,6)
# The regression coefficients of the AFT model
# can be tranformed into log(hazard ratios):
# coef.coxWeibull = - coef.weibull / shape.weibull
\dontrun{
set.seed(17)
da <- sim(ma,1000)
library(survival)
fa <- coxph(Surv(time,status)~sex+sbp,data=da)
coef(fa)
c(0.7,-0.008)/0.7
}
# The following are equivalent parametrizations
# which produce exactly the same random numbers:
model.aft <- lvm()
distribution(model.aft,"eventtime") <- weibull.lvm(intercept=-log(1/100)/2,sigma=1/2)
distribution(model.aft,"censtime") <- weibull.lvm(intercept=-log(1/100)/2,sigma=1/2)
sim(model.aft,6,seed=17)
model.aft <- lvm()
distribution(model.aft,"eventtime") <- weibull.lvm(scale=100^(1/2), shape=2)
distribution(model.aft,"censtime") <- weibull.lvm(scale=100^(1/2), shape=2)
sim(model.aft,6,seed=17)
model.cox <- lvm()
distribution(model.cox,"eventtime") <- coxWeibull.lvm(scale=1/100,shape=2)
distribution(model.cox,"censtime") <- coxWeibull.lvm(scale=1/100,shape=2)
sim(model.cox,6,seed=17)
# The minimum of multiple latent times one of them still
# being a censoring time, yield
# right censored competing risks data
mc <- lvm()
distribution(mc,~X2) <- binomial.lvm()
regression(mc) <- T1~f(X1,-.5)+f(X2,0.3)
regression(mc) <- T2~f(X2,0.6)
distribution(mc,~T1) <- coxWeibull.lvm(scale=1/100)
distribution(mc,~T2) <- coxWeibull.lvm(scale=1/100)
distribution(mc,~C) <- coxWeibull.lvm(scale=1/100)
mc <- eventTime(mc,time~min(T1=1,T2=2,C=0),"event")
sim(mc,6)
}
\author{
Thomas A. Gerds, Klaus K. Holst
}
\keyword{models}
\keyword{regression}
\keyword{survival}
|
