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### simMelanoma.R ---
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## author: Thomas Alexander Gerds
## created: Feb 27 2017 (09:52)
## Version:
## last-updated: May 26 2019 (10:55)
## By: Thomas Alexander Gerds
## Update #: 64
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##
### Commentary:
##
### Change Log:
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##
### Code:
##' Simulate data alike the Melanoma data
##'
##' This is based on the functionality of \code{library(lava)}.
##' @title Simulate data alike the Melanoma data
##' @param n sample size
##' @return data table of size n
##' @examples
##' set.seed(71)
##' simMelanoma(3)
##' @export
##' @author Thomas A. Gerds <tag@@biostat.ku.dk>
simMelanoma <- function(n){
ici=ici1=ici2=ici3=NULL
## data(Melanoma,package="riskRegression")
## Melanoma$ici1 <- 1*(Melanoma$ici=="1")
## Melanoma$ici2 <- 1*(Melanoma$ici=="2")
## Melanoma$ici3 <- 1*(Melanoma$ici=="3")
## pici <- prop.table(table(Melanoma$ici))
## pulcer <- prop.table(table(Melanoma$ulcer))
## pepicel <- prop.table(table(Melanoma$epicel))
## psex <- prop.table(table(Melanoma$sex))
## l0 <- glm(sex~ulcer+epicel+ici1+ici2+ici3,data=Melanoma,family="binomial")
## l1 <- glm(logthick~age+sex+ulcer+epicel+ici1+ici2+ici3,data=Melanoma)
## l2 <- glm(age~sex,data=Melanoma)
## G <- survival::survreg(Surv(time,status==0)~1,data=Melanoma)
## F1 <- survival::survreg(Surv(time,status==1)~logthick+age+sex+ulcer+epicel+ici1+ici2+ici3,data=Melanoma)
## F2 <- survival::survreg(Surv(time,status==2)~age+sex,data=Melanoma)
m <- lava::lvm(~ulcer+epicel+sex+age+logthick)
## m <- categorical(m,~ici, K=4,p=pici[-3])
lava::distribution(m,~age) <- lava::normal.lvm(mean=55,sd=10)
lava::distribution(m,~logthick) <- lava::normal.lvm(sd=0.8)
lava::distribution(m,~ici1) <- lava::binomial.lvm(p=0.29)
lava::distribution(m,~ici2) <- lava::binomial.lvm(p=0.52)
lava::distribution(m,~ici3) <- lava::binomial.lvm(p=0.11)
lava::distribution(m,~sex) <- lava::binomial.lvm(p=0.39)
lava::distribution(m,~ulcer) <- lava::binomial.lvm(p=0.44)
lava::distribution(m,~epicel) <- lava::binomial.lvm(p=0.44)
lava::distribution(m,~t0) <- lava::coxWeibull.lvm(scale=exp(-8/0.33),shape=1/0.33)
lava::distribution(m,~t1) <- lava::coxWeibull.lvm(scale=exp(-11.5/0.8),shape=1/0.8)
lava::distribution(m,~t2) <- lava::coxWeibull.lvm(scale=exp(-16/1.3),shape=1/1.3)
transform(m,thick~logthick) <- function(x){exp(x)}
lava::regression(m,sex~ulcer+epicel+ici1+ici2+ici3) <- c(0.83,0.67,-0.28,0.03,-0.28)
lava::regression(m,logthick~age+sex+ulcer+epicel+ici1+ici2+ici3) <- c(0.007,0.23,0.9,-0.35,0.56,0.73,0.83)
lava::regression(m,t1~logthick+age+sex+ulcer+epicel+ici1+ici2+ici3) <- -c(-0.29,-0.02,-0.34,-0.77,0.53,-1.39,-1.32,-1.7)/0.8
lava::intercept(m,"logthick") <- -1.3
lava::regression(m,t2~age+sex) <- -c(-0.08,-0.39)/1.3
m <- lava::eventTime(m,time~min(t0=0,t1=1,t2=2),"status")
simdat <- lava::sim(m,n)
data.table::setDT(simdat)
simdat[,ici:=factor("0",levels=0:3)]
simdat[ici1==1,ici:="1"]
simdat[ici2==1,ici:="2"]
simdat[ici3==1,ici:="3"]
simdat[,c("ici1","ici2","ici3","t0","t1","t2"):=NULL]
simdat$ici <- factor(simdat$ici)
simdat$ulcer <- factor(simdat$ulcer,levels=c("0","1"),labels=c("not present","present"))
simdat$epicel <- factor(simdat$epicel,levels=c("0","1"),labels=c("not present","present"))
simdat$sex <- factor(simdat$sex,levels=c("0","1"),labels=c("Female","Male"))
simdat
}
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### simMelanoma.R ends here
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