boot_ci_adj_cif: Bootstrap CI for adjusted CIF

In Lesly1031/AdjKM.CIF: A package for generating covariate-adjusted Kaplan-Meier and cumulative incidence functions

Bootstrap CI for adjusted CIF

Description

Use input data, time, status,grouping variables, adjusted covariates, events of interests, whether to use stratified model, and defining reference group as inputs

Usage

boot_ci_adj_cif(
  boot_n = 100,
  ci_cut = c(0.025, 0.975),
  data,
  time,
  status,
  group,
  covlist,
  event_code,
  stratified,
  reference_group
)

Arguments

boot_n	bootstrap sample size
ci_cut	default c(0.025, 0.975) bootstrap 95% CI
data	the input dataset
time	column name of time variable
status	column name of event status
group	grouping variable
covlist	list of covariates that should be included in the model
event_code	event of interests
stratified	"Yes" refers to use stratified model, "No" refers to use Fine and Gray regression
reference_group	NULL- unstratified FG when stratified = No; "G&B"- G&B when stratified = Yes; Otherwise, Storer's approach will be performed when using a self-defined reference

Value

Output is a dataframe with average number of adjusted CIF probabilities, as well as 2.5% and 97.5% percentiles.

Examples

library(KMsurv)
data(bmt)
bmt$arm <- bmt$group
bmt$arm = factor(as.character(bmt$arm), levels = c("2", "1", "3"))
bmt$z3 = as.character(bmt$z3)

bmt$CenCI <- 0
for (ii in 1:137) {
  if (bmt$d3[ii] == 0) {
    bmt$CenCI[ii] <- 0
  } else {
    if (bmt$d2[ii] == 1) {
      bmt$CenCI[ii] <- 1
    } else {
      bmt$CenCI[ii] <- 2
    }
  }
}

bmt$t2 = bmt$t2 * 12/365.25

# unstratified Fine-Gray regression model
result1_1 = boot_ci_adj_cif(boot_n = 100, ci_cut = c(0.025, 0.975), data = bmt, time = "t2",
 status = "CenCI", group = "arm", covlist = c("z1", "z3"), event_code = 1, "No",
                            NULL)

# stratified FG: Gail&Byar's approach
result1_2 = boot_ci_adj_cif(boot_n = 100, ci_cut = c(0.025, 0.975), data = bmt, time = "t2",
   status = "CenCI", group = "arm", covlist = c("z1", "z3"), event_code = 1, "Yes",
   "G&B")

 # stratified Storer
 result1_3 = boot_ci_adj_cif(boot_n = 100, ci_cut = c(0.025, 0.975), data = bmt, time = "t2",
    status = "CenCI", group = "arm", covlist = c("z1", "z3"), event_code = 1, "Yes",
   "arm:2")

Lesly1031/AdjKM.CIF documentation built on March 10, 2023, 12:02 p.m.