#'
#'
#'
#'
#'
#'
#'
verify_cancer <- function(partdata,
dx,wd=getwd(),remove=T){
#load the cancer registry
setwd(wd)
load("can.RData")
dx <- paste(dx,collapse="|")
##Subsetting the data to only cancer diagnoses of interest
can <- filter(can,
grepl(dx,ICD7) | grepl(dx,ICD9) | grepl(dx,ICDO10))
#Adding verified column to data
#A person is verified if its cancer diagnosis is recorded in the cancer registry or if its corresponding case
#is recorded in the cancer registry.
partdata <- partdata %>% mutate(verified =
(partdata$lop_nr %in% can$LopNr & partdata$case) |
partdata$lop_nr_case %in% can$LopNr)
#Giving data on the verification process
warning(with(partdata,sum(case & !verified))," (",round(with(partdata,sum(case & !verified)/sum(partdata$case)),digits = 2)*100,
"%) cases are not in the cancer registry. There are ",sum(!partdata$case & partdata$lop_nr %in% can$LopNr),
" controls that have a diagnosis of the given cancer.")
if(remove){
warning("These ",with(partdata,sum(case & !verified))," cases and their corresponding ",
with(partdata,sum(case & !verified))," controls have been removed.")
partdata <- partdata %>% filter(verified) %>% select(-verified)
}
return(partdata)
}
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