## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(Colossus)
library(data.table)
library(parallel)

## ----eval=FALSE---------------------------------------------------------------
#  df_Dose <- fread("EX_DOSE.csv")

## ----eval=FALSE---------------------------------------------------------------
#  col_list <- c("SES_CAT", "YOB_CAT", "dose_cat")
#  val <- factorize(df_Dose, col_list)
#  df_Dose <- val$df
#  
#  t0 <- "age_entry"
#  t1 <- "age_exit"
#  event <- "nonCLL"

## ----eval=FALSE---------------------------------------------------------------
#  # ERR
#  names <- c("cumulative_dose", "SES_CAT_1", "SES_CAT_2", "YOB_CAT_1", "YOB_CAT_2", "YOB_CAT_3", "YOB_CAT_4", "sexm")
#  tform <- c("plin", rep("loglin", length(names) - 1))
#  control <- list("Ncores" = 8, "maxiter" = 50, "verbose" = F)

## ----eval=FALSE---------------------------------------------------------------
#  e <- RunCoxRegression(df_Dose, t0, t1, event, names, tform = tform, control = control)

## ----eval=FALSE---------------------------------------------------------------
#  # HR
#  names <- c("cumulative_dose", "SES_CAT_1", "SES_CAT_2", "YOB_CAT_1", "YOB_CAT_2", "YOB_CAT_3", "YOB_CAT_4", "sexm")
#  tform <- rep("loglin", length(names))
#  e <- RunCoxRegression(df_Dose, t0, t1, event, names, tform = tform, control = control)
#  
#  # Categorical
#  names <- c("dose_cat_1", "dose_cat_2", "dose_cat_3", "dose_cat_4", "dose_cat_5", "dose_cat_6", "SES_CAT_1", "SES_CAT_2", "YOB_CAT_1", "YOB_CAT_2", "YOB_CAT_3", "YOB_CAT_4", "sexm")
#  tform <- rep("loglin", length(names))
#  e <- RunCoxRegression(df_Dose, t0, t1, event, names, tform = tform, control = control)