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seerStats<-function(canc,popsa) {
age=agedx=db=py=reg=cancer=over99=total=sex=year=seqnum=gte100=PY=NULL
# cf=function (x) comma_format()(x)
#seerStats(canc,popsae)
L=NULL
L$PDR=popsa%>%group_by(db,reg)%>%summarize(PY=round(sum(py)/1e6,1),age=weighted.mean(age,py))
L$PSY=popsa%>%group_by(sex,year)%>%summarize(PY=round(sum(py)/1e6,1))
D=canc%>%group_by(cancer,db)%>%summarize(n=n())
A=canc%>%filter(agedx>99.5)%>%group_by(cancer)%>%summarize(n=n())
canc$seqnum=ifelse(canc$seqnum>3,4,canc$seqnum)
canc$seqnum=ifelse(canc$seqnum==0,1,canc$seqnum)
Sq=canc%>%group_by(cancer,seqnum)%>%summarize(n=n())
C=dcast(D,cancer~db,value.var="n",fun.aggregate = sum,margins=c("db"))
# C=dcast(D,cancer~db,value.var="n",fun.aggregate = sum,margins=TRUE)
O=dcast(A,cancer~.,value.var="n")
S=dcast(Sq,cancer~seqnum,value.var="n",fun.aggregate = sum,margins=c("seqnum")) #checks fine with total
# S=dcast(Sq,cancer~seqnum,value.var="n")
d=left_join(C,O,by="cancer")
names(d)[5:6]=c("total","gte100")
d=d%>%mutate(under100=total-gte100)
d=left_join(d,S,by="cancer")
names(d)[8:12]=c("firsts","seconds","thirds","highers","all")
d[is.na(d)]=0
d$cancer=as.character(d$cancer)
d[dim(d)[1]+1,]=data.frame("total",t(sapply(d[-1],sum)))
d[dim(d)[1],1]="total"
L$d=d
cat(paste("\nTable 1. Cases per database, by >= or < 100, and by cancer sequence, through",
max(popsa$year),"(sexes and races pooled).\n"))
print(d)
cat(paste("\nTable 2. Population PY in millions and PY-weighted mean ages, through",
max(popsa$year),"(sexes and races pooled).\n"))
cat(paste(""))
print(as.data.frame(L$PDR))
N=sum(L$PSY$PY)
tit=paste(N,"Million Total Person-Years")
p=qplot(year,PY,col=sex,ylab="Person-Years (Millions)",main=tit,data=L$PSY)+
theme(legend.position = c(.18, .75),legend.title = element_blank(),legend.text=element_text(size=rel(1.5)),
axis.text=element_text(size=rel(2)),axis.title=element_text(size=rel(2)))
print(p)
invisible(L)
}
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