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simSeerSet<-function(N=2e9,yearEnd=2016,ka=1e-5,kb=0.04,Ab=1e-5,tauA=10,tauB=1,delay=1,period=4) {
# agedx=age=age86=canc=yrdx=sex=race=surv=modx=yrbrth=NULL
trt=cancers=NULL
data(stdUS, envir = environment())
# if (shape<1) {
# shape=1
# print("Warning: shape must be 1 or higher. It was less and is being set to 1. ")
# }
# N=2e9;yearEnd=2012;ka=1e-5;kb=0.04;Ab=1e-5;tauA=10;tauB=5;delay=1;period=4;shape=1;library(dplyr)
popsa=merge(data.frame(age=0.5:99.5),data.frame(year=1975:yearEnd))
popsa$py=N/40*SEERaBomb::stdUS$prop[round(popsa$age+0.5)]
# sum(popsa$py)
head(popsa)
# tail(popsa)
A=cbind(popsa[,1:2],cancers=rpois(dim(popsa)[1],ka*popsa$age*popsa$py))
head(A)
sum(A$cancers)
cancA=A[rep(seq_len(nrow(A)), times=A$cancers),]%>%select(-cancers)
cancA$surv=rexp(dim(cancA)[1],rate=1/tauA)
cancA$yrdx=cancA$year+runif(dim(cancA)[1],max=0.9999)
head(cancA,10)
# cancA$surv=runif(dim(cancA)[1],0,20)
# mean(cancA$surv)
trimSurv=function(x) {
x$surv=ifelse(x$surv+x$age>123,123-x$age,x$surv)
x$surv=ifelse(x$surv+x$yrdx>yearEnd+0.9999,yearEnd+0.9999-x$yrdx,x$surv)
x
}
cancA=trimSurv(cancA)
cancA$cancer="A"
trts=c("noRad","rad")
cancA$trt=sample(trts,dim(cancA)[1],replace=T)
cancA$casenum=1:dim(cancA)[1]
cancA$seqnum=0
table(cancA$trt)
# rownames(cancA)=cancA$casenum # can't do as rownames since IDs are not unique
head(cancA)
###### treatment of A with rad induces B
cancAr=cancA%>%filter(trt=="rad")
py=cancAr$surv
py=ifelse(py<=delay,0,py-delay)
py=ifelse(py>=period,period,py)
cancAr$seconds=rpois(dim(cancAr)[1],4*(Ab/kb)*(exp(kb*(cancAr$age+py+delay))-exp(kb*(cancAr$age+delay)) ) )
sum(cancAr$seconds)
cancAr$seqnum[cancAr$seconds>0]=1
cancBAr=cancAr[cancAr$seconds>0,]
cancBAr$seqnum=2
cancBAr$cancer="B"
cancBAr$trt="noRad"
py=py[cancAr$seconds>0]
Y=runif(dim(cancBAr)[1],Ab*exp(kb*(cancBAr$age+delay)),Ab*exp(kb*(cancBAr$age+py+delay)))
ages=(log(Y)-log(Ab))/kb
cancBAr$yrdx=cancBAr$yrdx+ages-cancBAr$age
# cancBA$yrdx=cancBA$yrdx+delay+period*rbeta(dim(cancBA)[1],shape,shape)
# cancBA$yrdx=cancBA$yrdx+runif(dim(cancBA)[1],delay+1e-4,delay+period-1e-4)
# cancBA$yrdx=cancBA$yrdx+ runif(dim(cancBA)[1],delay,delay+period)
# cancBA$yrdx=cancBA$yrdx+pmin(runif(dim(cancBA)[1],delay,delay+period),cancBA$surv)
cancBAr$seconds=NULL
cancAr$seconds=NULL
cancA[cancA$casenum%in%cancAr$casenum,]=cancAr
# hist(rbeta(1e4,1,1))
# hist(rbeta(1e4,4,4))
######now background B after A cases
py=cancA$surv
cancA$seconds=rpois(dim(cancA)[1],(Ab/kb)*(exp(kb*(cancA$age+py))-exp(kb*cancA$age) ) )
sum(cancA$seconds)
# table(cancA$seconds,cut(py,breaks=seq(0,4,0.1)))
cancA$seqnum[cancA$seconds>0]=1
cancBA=cancA[cancA$seconds>0,]
py=py[cancA$seconds>0]
cancBA$seqnum=2
cancBA$cancer="B"
Y=runif(dim(cancBA)[1],Ab*exp(kb*cancBA$age),Ab*exp(kb*(cancBA$age+py)))
ages=(log(Y)-log(Ab))/kb
cancBA$yrdx=cancBA$yrdx+ages-cancBA$age
# range(ages)
# head(cancBA)
# cancBA$yrdx=cancBA$yrdx+runif(dim(cancBA)[1],0,py)
cancBA$seconds=NULL
cancA$seconds=NULL
head(cancBA)
# head(cancA)
######now background B
B=cbind(popsa[,1:2],cancers=rpois(dim(popsa)[1],Ab*exp(kb*popsa$age)*popsa$py))
cancB=B[rep(seq_len(nrow(B)), times=B$cancers),]%>%select(-cancers)
cancB$surv=rexp(dim(cancB)[1],rate=1/tauB)
cancB$yrdx=cancB$year+runif(dim(cancB)[1],max=0.9999)
cancB=trimSurv(cancB)
cancB$cancer="B"
cancB$trt=sample(trts,dim(cancB)[1],replace=T)
cancB$casenum=(1e7+1):(1e7+dim(cancB)[1])
cancB$seqnum=0
head(cancB)
###### merge in B
canc=rbind(cancA,cancBAr)
canc=rbind(canc,cancBA)
canc=rbind(canc,cancB)
head(canc)
tail(canc)
table(canc$seqnum)
canc$trt=factor(canc$trt)
canc$cancer=factor(canc$cancer)
head(canc)
cancerS=levels(canc$canc)
# sapply(canc,class)
canc=tbl_df(canc)
popsa=tbl_df(popsa)
# and package it all up
seerSet=list(canc=canc,popsa=popsa,ageStart=min(popsa$age),ageEnd=max(popsa$age),sex="neut",race="neut",
cancerS=cancerS,yearEnd=max(popsa$year))
class(seerSet)="seerSet"
seerSet
} # return a list that can be attached or with-ed in other functions
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