setwd("~/Desktop/cdsc/health literacy/")

mapping = read.delim("Mapping - Sheet1.tsv")
mapping <- mapping[,colnames(mapping) != "Notes"]

IHME = read.csv("IHME_Data.csv")
best <- read.csv("Best_Data.csv")

# first, create the list of all the one-to-ones
d <- merge(best, mapping[!is.na(mapping$Mapping_Type) & mapping$Mapping_Type == "one-to-one",], by.x="Reconciled_Name", by.y="Best_Disease_Name", all=TRUE)


# now merge the imhe data on
d <-  merge(d, IHME[IHME$measure_name == "DALYs (Disability-Adjusted Life Years)", 
                  c("cause_id", "measure_name", "year", "val")],
          by.x=c("IHME_Cause_ID", "Year"),
          by.y=c("cause_id", "year"))
# next, handle the one-to-manys but summing up