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incidSEER=function(canc,popsae,cancers) {
cancer=sex=race=agedx=yrdx=year=age=py=cases=NULL
# load("~/data/SEER/mrgd/popsae.RData") # loads in popsae (extended to ages 85-99)
# load("~/data/SEER/mrgd/cancDef.RData") #loads in canc
# library(tidyverse)
# cancers="CMML"
# cancers=c("CML","CMML")
startYrs=c(CMML=1993,MDS=2001,NOS=2001,RA=2001,RAEB=2001,RARS=2001,Del5q=2001,LGL=2010)
(startYrs=c(startYrs,MPN=2001,unknown=2001,AMLti=2001,LGL=2010))
(outnms=setdiff(cancers,names(startYrs)))
x=rep(1975,length(outnms))
names(x)<-outnms
(startYrs=c(startYrs,x))
D=canc%>%select(cancer,sex,race,agedx,year=yrdx)%>%mutate(age=agedx+0.5)%>%filter(cancer%in%cancers)%>%select(-agedx)
# reshape2::dcast(d%>%group_by(cancer,year)%>%summarize(n=n()),cancer~year)
m=D%>%group_by(cancer,sex,race,age,year)%>%summarise(n=n())
p=popsae%>%group_by(sex,race,age,year)%>%summarise(py=sum(py))
s=data.frame(sex=sort(unique(m$sex)))
# r=data.frame(race=sort(unique(m$race))) # skip since race is in automatically, like age and year
c=data.frame(cancer=cancers)
cs=merge(c,s)%>%arrange(cancer,sex)
# csr=merge(cs,r)%>%arrange(cancer,sex,race) #comment to keep label of race
options(warn=-1)
pL=left_join(cs,p,by="sex")
d=left_join(pL,m)
options(warn=0)
d[is.na(d$n),"n"]=0 #join left missings where zero's should be, so fix this
# head(d)
d=d%>%group_by(cancer)%>%filter(year>=startYrs[as.character(cancer[1])])
# reshape2::dcast(d%>%group_by(cancer,year)%>%summarize(n=sum(n)),cancer~year) #check, should be same
d%>%mutate(py=py/1e5,incid=n/py)
}
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