boot_ci_adj_km: 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_km(
  boot_n = 100,
  ci_cut = c(0.025, 0.975),
  data,
  time,
  status,
  group,
  covlist,
  stratified_cox,
  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
stratified_cox	"Yes" refers to use stratified model, "No" refers to use coxph regression
reference_group	NULL- unstratified coxph 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 survival probabilities, as well as 2.5% and 97.5% percentiles.

Examples

# Data preparation
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$t2 = bmt$t2 * 12/365.25

# Unstratified cox
result1_1 = boot_ci_adj_km(boot_n = 100, ci_cut = c(0.025, 0.975), data = bmt, time = "t2",
status = "d3", group = "arm", covlist = c("z1", "z3"), stratified_cox = "No",
reference_group = NULL)

# Stratified Cox: Gail and Byar's method
result1_2 = boot_ci_adj_km(boot_n = 100, ci_cut = c(0.025, 0.975), data = bmt, time = "t2",
status = "d3", group = "arm", covlist = c("z1", "z3"), stratified_cox = "Yes",
reference_group = "G&B")

# Stratified Cox: Storer's approach
result1_3 = boot_ci_adj_km(boot_n = 100, ci_cut = c(0.025, 0.975), data = bmt, time = "t2",
status = "d3", group = "arm", covlist = c("z1", "z3"), stratified_cox = "Yes",
reference_group = "arm:2")

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