getSurvData: Transform to survival data format
In n8thangreen/HESmanip: Hospital length of stay data preprocessing and analysis

Create a simpler survival analysis format array; basically a subset of the total.data columns with the dates removed so all time origins are equal.

1	getSurvData(total.data)

total.data

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (total.data) 
{
    survData <- within(total.data, {
        time <- as.numeric(adm_diff_dis)
        event <- hes_dischargeddeadoralive == "Death"
        age <- hes_ageatstartofepisode
        gender <- droplevels(hes_sexdescription)
        spectime <- as.numeric(adm_diff_specdate)
        agegr <- cut(age, breaks = c(0, 2, 5, 10, 18, 40, 60, 
            100, 10000))
        rm(lab_opieid, hes_ID, lab_Specimendate, hes_admdte, 
            hes_disdte, adm_diff_specdate, dis_diff_specdate, 
            hes_dismethdescription, adm_diff_dis, hes_sexdescription, 
            hes_ageatstartofepisode, hes_dischargeddeadoralive, 
            lab_organismname, lab_group, Gram)
    })
    survData$age[survData$age > 1000] <- 0
    survData$agegr <- factor(survData$agegr, c("(100,1e+04]", 
        "(0,2]", "(2,5]", "(5,10]", "(10,18]", "(18,40]", "(40,60]", 
        "(60,100]"))
    survData <- subdistn(survData)
    survData
  }