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
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, "change_all" = TRUE,
"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")
#> [1] TRUE