data-raw/smart.R

In road2stat/hdnom: Benchmarking and Visualization Toolkit for Penalized Cox Models

# Generate the `smart` dataset by imputing the original SMART study data
library("hdnom")
library("mice")
library("Hmisc")

data("smarto")
set.seed(1000)

smarti <- aregImpute(
  ~ I(TEVENT) + EVENT + SEX + I(AGE) +
    DIABETES + CEREBRAL + CARDIAC + AAA + PERIPH +
    STENOSIS + SYSTBP + DIASTBP + SYSTH + DIASTH +
    I(LENGTH) + I(WEIGHT) + I(BMI) +
    I(CHOL) + I(HDL) + I(LDL) + I(TRIG) + I(HOMOC) + I(GLUT) + I(CREAT) + I(IMT) +
    as.factor(ALBUMIN) + as.factor(SMOKING) + I(PACKYRS) + as.factor(ALCOHOL),
  n.impute = 10, data = smarto
)

imputed <- impute.transcan(
  smarti,
  imputation = 1, data = smarto,
  list.out = TRUE, pr = FALSE, check = FALSE
)
smart <- smarto
smart[names(imputed)] <- imputed
str(smart)

save(smart, file = "data/smart.rda")