calculate_trt_effect {bunsen}R Documentation

Calculate the marginal treatment effect using counterfactual simulations

Description

This function is used to calculate the logHR using cox model after obtaining the counterfactural simulations for potential outcomes from simulate_counterfactuals.

Usage

calculate_trt_effect(sim_out_1d, sim_out_0d, sim_out_1c, sim_out_0c)

Arguments

sim_out_1d

List. A list from simulate_counterfactuals for cox_event in treatment group, e.g. the cox model using OS.

sim_out_0d

List. A list from simulate_counterfactuals for cox_event in control group, e.g. the cox model using OS.

sim_out_1c

List. A list from simulate_counterfactuals for cox_event in treatment group, e.g. the cox model using 1-OS.

sim_out_0c

List. A list from simulate_counterfactuals for cox_event in control group, e.g. the cox model using 1-OS.

Details

The event indicator from this function uses the equation 10', I(Y0<Y0_cens) or I(Y1<Y1_cens).

Value

The marginal beta (logHR)

References

Daniel R, Zhang J, Farewell D. Making apples from oranges: Comparing noncollapsible effect estimators and their standard errors after adjustment for different covariate sets. Biom J. 2021;63(3):528-557. doi:10.1002/bimj.201900297

Examples

library(survival)
data("oak")

cox_event <- coxph(Surv(OS, os.status) ~ trt + btmb + pdl1, data = oak)
#
cox_censor <- coxph(Surv(OS, 1 - os.status) ~ trt + btmb + pdl1, data = oak)
bh <- basehaz(cox_event, centered = FALSE)
bh_c <- basehaz(cox_censor, centered = FALSE)
s_condi <- calculate_statistics(model = cox_event, trt = "trt")
s_condi_c <- calculate_statistics(model = cox_censor, trt = "trt")
sim_out_1d <- simulate_counterfactuals(
bh = bh, surv_cond = s_condi$surv_cond1, cpp = FALSE, M = 1000)
sim_out_0d <- simulate_counterfactuals(
bh = bh, surv_cond = s_condi$surv_cond0, cpp = FALSE, M = 1000)
sim_out_1c <- simulate_counterfactuals(
bh = bh_c, surv_cond = s_condi_c$surv_cond1, cpp = FALSE, M = 1000)
sim_out_0c <- simulate_counterfactuals(
bh = bh_c, surv_cond = s_condi_c$surv_cond0, cpp = FALSE, M = 1000)

output <- calculate_trt_effect(sim_out_1d, sim_out_0d, sim_out_1c, sim_out_0c)


[Package bunsen version 0.1.0 Index]