## 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)
}
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