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

## ----setup--------------------------------------------------------------------
Sys.setenv(OMP_THREAD_LIMIT = 1) # Reducing core use, to avoid accidental use of too many cores
library(Colossus)
library(data.table)

## -----------------------------------------------------------------------------
# Each model has entry and exit columns, t0 and t1
# Events are in a column called lung
# The hazard ratio has both an exponential and linear dependence
Model_Eq <- Cox(t0, t1, lung) ~ loglinear(dose0, dose1, 0) +
  linear(dose2, 1) + ME()
Model_Eq <- Cox(t0, t1, lung) ~ loglinear(dose0, dose1) +
  linear(dose2, 1)

df <- data.table(
  dose0 = 1:4, dose1 = 2:5, dose2 = 3:6,
  t0 = c(0, 0, 1, 0), t1 = 5:8, lung = c(1, 0, 0, 1)
)
res <- get_form(Model_Eq, df, nthreads = 1)
formula <- res$model
new_data <- res$data