R/defineVariables.R

In DALY: The DALY Calculator - Graphical User Interface for Probabilistic DALY Calculation in R

## Set standard values

defineVariables <-
function(){
  DALYassign("ageGroups", c("0-4", "5-14", "15-44", "45-59", "60+"))
  DALYassign("fixed", c("Age Group", "Male", "Female"))
  DALYassign("txtLBL", c("INCIDENCE", "TREATMENT", "ONSET",
                         "DURATION", "DWtreated", "DWuntreated",
                         "MORTALITY", "AvgAgeDeath"))
  DALYassign("txtLbl", c("Inc", "Trt", "Ons", "Dur",
                         "DWt", "DWn", "Mrt", "Lxp"))
  DALYassign("txtlbl", c("inc", "trt", "ons", "dur",
                         "DWt", "DWn", "mrt", "lxp"))
  DALYassign("distributions", c("Beta-Pert", "Beta", "Gamma", "Normal",
                                "LogNormal.geom", "LogNormal.arithm",
                                "Uniform", "Fixed"))
  DALYassign("stratifications", c("Age and Sex", "Age", "Sex", "None"))
  DALYassign("ages", c(0, 1, 5, 10, 15, 20, 25,
                       30, 35, 40, 45, 50, 55, 60,
                       65, 70, 75, 80, 85, 90, 95))

  ## standard life expectancy tables
  DALYassign("stdLEtab", tclVar("GBD2010"))

  ## GBD1990 (Coale-Demeny model life table, west)
  DALYassign("stdM", c(80.00, 79.36, 75.38, 70.40, 65.41, 60.44, 55.47,
                       50.51, 45.57, 40.64, 35.77, 30.99, 26.32, 21.81,
                       17.50, 13.58, 10.17,  7.45,  5.24,  3.54,  2.31))
  DALYassign("stdF", c(82.50, 81.84, 77.95, 72.99, 68.02, 63.08, 58.17,
                       53.27, 48.38, 43.53, 38.72, 33.99, 29.37, 24.83,
                       20.44, 16.20, 12.28,  8.90,  6.22,  4.25,  2.89))

  ## GBD 2010 (synthetic life table)
  DALYassign("stdGBD", c(86.02, 85.21, 81.25, 76.27, 71.29, 66.35, 61.40,
                         56.46, 51.53, 46.64, 38.00, 33.32, 28.73, 24.20,
                         19.80, 15.62, 11.75,  8.31,  4.00,  2.66,  1.87))

  ## WHO/GHE (projected frontier life table, 2050)
  DALYassign("stdWHO", c(91.94, 91.00, 87.02, 82.03, 77.04, 72.06, 67.08,
                         62.11, 57.15, 52.20, 47.27, 42.36, 37.49, 32.65,
                         27.86, 23.15, 18.62, 14.41, 10.70,  7.60,  5.13))

  ## 'pop' = Population matrix
  .pop <- tclArray()
  for(x in seq(0, 2))
    .pop[[0, x]] <- DALYget("fixed")[x+1]
  for(y in seq(5))
    .pop[[y, 0]] <- DALYget("ageGroups")[y]
  DALYassign(".pop", .pop)
  DALYassign("pop", matrix(nrow = 5, ncol = 2))

  ## 'LE' = Life Expectancy table
  .LE <- tclArray()
  .LE[[0, 0]] <- "Age"
  for(x in seq(2)) .LE[[0, x]] <- DALYget("fixed")[x+1]
  for(y in seq(21)) .LE[[y, 0]] <- DALYget("ages")[y]
  DALYassign(".LE", .LE)

  DALYassign("LE", matrix(nrow = 21, ncol = 2))
  setStdLE()

  ## Set 'data', 'dist' & 'strat'
  distList <- c(3, 2, 8, 8, 2, 2, 3, 8)
  for (i in seq(8)){
    for (j in seq(8)){
      ## 'txtlbl' + 'i' = parameters per outcome
      DALYassign(paste(".", DALYget("txtlbl")[j], i, sep = ""),
                 tclArray())
      DALYassign(paste(DALYget("txtlbl")[j], i, sep = ""),
                 matrix(nrow = 6, ncol = 5))

      ## 'strat' + 'txtLbl' + 'i' = stratification per parameter per outcome
      DALYassign(paste(".strat", DALYget("txtLbl")[j], i, sep = ""),
                 tclVar(DALYget("stratifications")[1]))
      DALYassign(paste("strat", DALYget("txtLbl")[j], i, sep = ""),
                 DALYget("stratifications")[1])

      ## 'distributions' + 'txtLbl' + 'i' = dist per parameter per outcome
      d <- distList[j]
      DALYassign(paste(".dist", DALYget("txtLbl")[j], i, sep = ""),
                 tclVar(DALYget("distributions")[d]))
      DALYassign(paste("dist", DALYget("txtLbl")[j], i, sep = ""),
                 DALYget("distributions")[d])
    }

    ## assign 'ageGroups' labels to '.txtlbl' + 'i'
    for (j in seq(5)){
      for(k in seq(8)){
        DALYeval(parse(text = paste(".", DALYget("txtlbl")[k], i,
                                    "[[", j, ",0]] <- '",
                                    DALYget("ageGroups")[j], "'", sep = "")))
      }
    }
  }

  ## assign 'disease' and 'outcome' names
  DALYassign("diseaseName", tclVar())
  for (i in seq(8))
    DALYassign(paste("outcome", i, "Name", sep = ""), tclVar())

  ## assign 'aw' and 'dr' variables
  DALYassign(".aw", tclVar("No"))
  DALYassign(".dr", tclVar("0"))

  ## assign 'option' variables
  DALYassign(".it", tclVar("20000"))
  DALYassign(".optOP", tclVar("Summed over age/sex classes"))
  DALYassign(".optOC", tclVar("Summed over outcomes"))
  DALYassign(".optRA", tclVar("Absolute"))
  DALYassign(".optHist", tclVar("1"))
  DALYassign("it", 20000)
  DALYassign("optOP", "Summed over age/sex classes")
  DALYassign("optOC", "Summed over outcomes")
  DALYassign("optRA", "Absolute")
  DALYassign("optHist", 1)
}