Colossus (version 1.2)

GetCensWeight: Calculates and returns data for time by hazard and survival to estimate censoring rate

Description

GetCensWeight uses user provided data, time/event columns, vectors specifying the model, and options generate an estimate of the censoring rate, plots, and returns the data

Usage

GetCensWeight(
  df,
  time1,
  time2,
  event0,
  names,
  term_n,
  tform,
  keep_constant,
  a_n,
  modelform,
  fir,
  control,
  plot_options,
  model_control = list(),
  strat_col = "e"
)

Value

saves the plots in the current directory and returns a data.table of time and corresponding hazard, cumulative hazard, and survival

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

names

columns for elements of the model, used to identify data columns

term_n

term numbers for each element of the model

tform

list of string function identifiers, used for linear/step

keep_constant

binary values to denote which parameters to change

a_n

list of initial parameter values, used to determine number of parameters. May be either a list of vectors or a single vector.

modelform

string specifying the model type: M, ME, A, PA, PAE, GMIX, GMIX-R, GMIX-E

fir

term number for the initial term, used for models of the form T0*f(Ti) in which the order matters

control

list of parameters controlling the convergence, see Def_Control() for options or vignette("Control_Options")

plot_options

list of parameters controlling the plot options, see RunCoxPlots() for different options

model_control

controls which alternative model options are used, see Def_model_control() for options and vignette("Control_Options") for further details

strat_col

column to stratify by if needed

Examples

library(data.table)
## basic example code reproduced from the starting-description vignette
df <- data.table::data.table(
  "UserID" = c(112, 114, 213, 214, 115, 116, 117),
  "Starting_Age" = c(18, 20, 18, 19, 21, 20, 18),
  "Ending_Age" = c(30, 45, 57, 47, 36, 60, 55),
  "Cancer_Status" = c(0, 0, 1, 0, 1, 0, 0),
  "a" = c(0, 1, 1, 0, 1, 0, 1),
  "b" = c(1, 1.1, 2.1, 2, 0.1, 1, 0.2),
  "c" = c(10, 11, 10, 11, 12, 9, 11),
  "d" = c(0, 0, 0, 1, 1, 1, 1)
)
# For the interval case
time1 <- "Starting_Age"
time2 <- "Ending_Age"
event <- "Cancer_Status"
names <- c("a", "b", "c", "d")
term_n <- c(0, 1, 1, 2)
tform <- c("loglin", "lin", "lin", "plin")
modelform <- "M"
fir <- 0
a_n <- c(0.1, 0.1, 0.1, 0.1)
keep_constant <- c(0, 0, 0, 0)
der_iden <- 0
df$censor <- (df$Cancer_Status == 0)
event <- "censor"
control <- list(
  "ncores" = 2, "lr" = 0.75, "maxiter" = 20, "halfmax" = 5,
  "epsilon" = 1e-6, "deriv_epsilon" = 1e-6,
  "abs_max" = 1.0, "change_all" = TRUE, "dose_abs_max" = 100.0, "verbose" = FALSE,
  "ties" = "breslow", "double_step" = 1
)
plot_options <- list(
  "name" = paste(tempfile(), "run_06", sep = ""), "verbose" = FALSE,
  "studyID" = "studyID", "age_unit" = "years"
)
dft <- GetCensWeight(
  df, time1, time2, event, names, term_n, tform,
  keep_constant, a_n, modelform, fir, control, plot_options
)
t_ref <- dft$t
surv_ref <- dft$surv
t_c <- df$t1
cens_weight <- approx(t_ref, surv_ref, t_c, rule = 2)$y