如何解决将 ggforest 与 Coxme 主题一起使用
我希望使用我从 ggforest
函数获得的混合效应 cox 回归生成一个 coxme
图。但是,当我使用 ggforest() 函数时,它说这仅适用于 coxph
主题,而不适用于 coxme
主题。
请允许我用我在 here 找到的案例来说明示例:
########## simulate data ##########
set.seed(10)
N <- 250
dat <- data.frame(ID = factor(1:N),age = rnorm(N,mean = 45,sd = 5),sex = sample(0:1,N,TRUE),basemort = rnorm(N,sd = 3))
interval <- matrix(sample(2:14,N * 3,replace = TRUE),N)
windows <- t(apply(cbind(0,interval),1,cumsum))
windows <- rbind(windows[,1:2],windows[,2:3],3:4])
colnames(windows) <- c("time1","time2")
dat <- cbind(do.call(rbind,rep(list(dat),3)),windows)
dat <- dat[order(dat$ID),]
dat$assessment <- rep(1:3,N)
rownames(dat) <- NULL
# simulate survival (mortality) data
transplant <- with(dat,{
mu <- (0.05 * age) + (0.3 * time2)
lp <- rnorm(N * 3,mean = mu,sd = 1)
as.integer(lp > quantile(lp,probs = 0.65))
})
# ensure that transplants do not revert
transplant <- as.integer(ave(transplant,dat$ID,FUN = cumsum) >= 1)
# simulate survival (mortality) data
mortality <- with(dat,{
mu <- basemort + (0.05 * age) - (2.5 * sex) + (0.3 * time2)
lp <- rnorm(N * 3,sd = 1)
as.integer(lp > median(lp))
})
# ensure that once someone dies,he or she stays dead
mortality <- as.integer(ave(mortality,FUN = cumsum) >= 1)
# ensure no one dead at baseline
mortality[dat$assessment == 1] <- 0
# ensure no post mortem change in transplant status
transplant <- unlist(by(data.frame(mortality,transplant),FUN = function(x) {
i <- cumsum(x$mortality)
tstat <- x$transplant[i == 1]
x$transplant[i >= 1] <- tstat
return(x$transplant)
}))
dat$transplant <- transplant
dat$mortality <- mortality
library(dplyr)
dat = dat%>%
mutate(age.gp = ifelse(age >=30 & age < 40,ifelse(age >=40 & age< 50,2,3)))
dat$age.gp <- factor(dat$age.gp,levels = c("1","2","3"),labels = c("30 - 39","40-49","50 above"))
m <- coxph(Surv(time1,time2,mortality) ~ age + sex + transplant,data = dat)
########## cox model with random effects ########## given repeated
########## observations on individuals each individual likely has their
########## own baseline so adjust with a mixed effects cox model using
########## the coxme package
m4 <- coxme(Surv(time1,mortality) ~ age + sex + transplant + (1 |
ID),data = dat)
我在这里以模型 m
制作了一个 ggforest 图。我如何在此 ggforest 图中使用 m4
中产生的估计值?谢谢!
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