gen_time_dep: Applies time dependence to parameters

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

Applies time dependence to parameters

Description

gen_time_dep generates a new dataframe with time dependent covariates by applying a grid in time

Usage

gen_time_dep(
  df,
  time1,
  time2,
  event0,
  iscox,
  dt,
  new_names,
  dep_cols,
  func_form,
  fname,
  tform,
  nthreads = as.numeric(detectCores())
)

Arguments

df	a data.table containing the columns of interest
time1	column used for time period starts
time2	column used for time period end
event0	column used for event status
iscox	boolean if rows not at event times should not be kept, rows are removed if true. a Cox proportional hazards model does not use rows with intervals not containing event times
dt	spacing in time for new rows
new_names	list of new names to use instead of default, default used if entry is ”"
dep_cols	columns that are not needed in the new dataframe
func_form	vector of functions to apply to each time-dependent covariate. Of the form func(df, time) returning a vector of the new column value
fname	filename used for new dataframe
tform	list of string function identifiers, used for linear/step
nthreads	number of threads to use, do not use more threads than available on your machine

Value

returns the updated dataframe

See Also

Other Data Cleaning Functions: Check_Dupe_Columns(), Check_Trunc(), Check_Verbose(), Convert_Model_Eq(), Correct_Formula_Order(), Date_Shift(), Def_Control(), Def_Control_Guess(), Def_model_control(), Def_modelform_fix(), Event_Count_Gen(), Event_Time_Gen(), Joint_Multiple_Events(), Replace_Missing(), Time_Since(), factorize(), factorize_par(), interact_them()

Examples

library(data.table)
# Adapted from the tests
a <- c(20, 20, 5, 10, 15)
b <- c(1, 2, 1, 1, 2)
c <- c(0, 0, 1, 1, 1)
df <- data.table::data.table("a" = a, "b" = b, "c" = c)
time1 <- "%trunc%"
time2 <- "a"
event <- "c"
control <- list(
  "lr" = 0.75, "maxiter" = -1, "halfmax" = 5, "epsilon" = 1e-9,
  "deriv_epsilon" = 1e-9, "abs_max" = 1.0,
  "dose_abs_max" = 100.0,
  "verbose" = FALSE, "ties" = "breslow", "double_step" = 1
)
grt_f <- function(df, time_col) {
  return((df[, "b"] * df[, get(time_col)])[[1]])
}
func_form <- c("lin")
df_new <- gen_time_dep(
  df, time1, time2, event, TRUE, 0.01, c("grt"), c(),
  c(grt_f), paste("test", "_new.csv", sep = ""), func_form, 2
)
file.remove("test_new.csv")

Colossus documentation built on June 8, 2025, 1:10 p.m.