Nothing
incidAbomb=function(d) {
py=O=.=NULL
# load("~/data/abomb/abomb.RData")
# head(heme,2)
# library(tidyverse)
# # (d=heme%>%select(ageG:DG,py,AML=AMLtot,ALL,CML))
# (d=heme%>%select(ageG:DG,D,py,AML=AMLtot,ALL,CML))
# d=d%>%group_by(ageG,DG)
nms=names(d)
if (!"DG"%in%nms) stop("Dose group column DG must be in d.")
if (!"py"%in%nms) stop("Person-years column py must be in d.")
end1=which(nms=="DG")
start3=which(nms=="py")
n=length(nms)
hd=nms[1:end1]
sums=nms[start3:n]
cancers=sums[-1]
if ("upy"%in%nms) cancers=cancers[-1]
if ("subjects"%in%nms) cancers=cancers[-1]
(mnsBlkNotEmpty=start3>(end1+1))
if (mnsBlkNotEmpty) means=nms[(end1+1):(start3-1)]
(ds=d%>%summarize_at(vars(sums),funs(sum)))
if (mnsBlkNotEmpty) (dm=d%>%summarize_at(vars(means),funs(weighted.mean(.,w=py))))
if (mnsBlkNotEmpty) D=left_join(dm,ds) else #like bind_cols() but removes extra col copies
D=ds
options(warn=-1) #warning about column labels expected in next line
D=D%>%tidyr::gather(value="O",key="cancer",cancers)#O=Observed
options(warn=0)
D$cancer=factor(D$cancer,levels=cancers)#set order
tibble::as_tibble(D%>%mutate(py=py/1e5,I=O/py,LL=qpois(0.025,O)/py,UL=qpois(0.975,O)/py))
}
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