Calculate the adjusted CIF probability

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

adjusted_CIF(
  data,
  time,
  status,
  group,
  covlist,
  event_code = 1,
  stratified = "Yes",
  reference_group = "G&B"
)

Arguments

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 adjusted CIF probabilities. If the PH assumption is invalid or if practitioners need a method by which the event time points of the adjusted function match those of the unadjusted function, the stratified model should be used (Gail and Byar and Storer et. al), otherwise, unstratified FG model can be used.

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 FG
result1 = adjusted_CIF(data = bmt, time = "t2", status = "CenCI", group = "arm",
covlist = c("z1", "z3"), event_code = 1, stratified = "No", reference_group = NULL)
# stratified G&B
result2 = adjusted_CIF(data = bmt, time = "t2", status = "CenCI", group = "arm",
covlist = c("z1", "z3"), event_code = 1, stratified = "Yes", reference_group = "G&B")
# stratified Storer
result3 = adjusted_CIF(data = bmt, time = "t2", status = "CenCI", group = "arm",
covlist = c("z1", "z3"), event_code = 1, stratified = "Yes", reference_group = "arm:2")