inst/doc/Script_Comparison_Epicure.R

In Colossus: "Risk Model Regression and Analysis with Complex Non-Linear Models"

## ----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" = 100, "verbose" = 2, "epsilon" = 1e-9, "der_epsilon" = 1e-9)

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

## ----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)
# Interpret_Output(e)
# 
# # 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)
# Interpret_Output(e)