hist_combo3: Dataset: historical and concurrent data on a three-way...

In OncoBayes2: Bayesian Logistic Regression for Oncology Dose-Escalation Trials

Dataset: historical and concurrent data on a three-way combination

Description

This dataset involves a hypothetical dose-escalation study of combination therapy with three treatment components. From two previous studies HistAgent1 and HistAgent2, historical data is available on each of the treatments as single-agents, as well as two of the two-way combinations. However, due to a difference in treatment schedule between the Combo study and the historical studies, a stratification (through stratum_id) is made between the groups to allow differential discounting of the alternate-dose data.

Usage

hist_combo3

Format

A data frame with 18 rows and 7 variables:

group_id

study

drug_A

dose of Drug A

drug_B

dose of Drug B

drug_C

dose of Drug C

num_patients

number of patients

num_toxicities

number of DLTs

stratum_id

stratum for group_id's used for differential discounting

Examples

## Setting up dummy sampling for fast execution of example
## Please use 4 chains and 100x more warmup & iter in practice
.user_mc_options <- options(OncoBayes2.MC.warmup=10, OncoBayes2.MC.iter=20, OncoBayes2.MC.chains=1,
                            OncoBayes2.MC.save_warmup=FALSE)

## example combo3

library(abind)

dref <- c(500, 500, 1000)
num_comp <- 3
num_inter <- choose(3,2) + 1
num_strata <- nlevels(hist_combo3$stratum_id)
num_groups <- nlevels(hist_combo3$group_id)

blrmfit <- blrm_exnex(
  cbind(num_toxicities, num_patients-num_toxicities) ~
    1 + I(log(drug_A/dref[1])) |
    1 + I(log(drug_B/dref[2])) |
    1 + I(log(drug_C/dref[3])) |
    0
  + I(drug_A/dref[1] * drug_B/dref[2])
  + I(drug_A/dref[1] * drug_C/dref[3])
  + I(drug_B/dref[2] * drug_C/dref[3])
  + I(drug_A/dref[1] * drug_B/dref[2] * drug_C/dref[3]) |
    stratum_id/group_id,
  data = hist_combo3,
  prior_EX_mu_mean_comp = matrix(c(logit(1/3), 0), nrow = num_comp, ncol = 2, TRUE),
  prior_EX_mu_sd_comp = matrix(c(2, 1), nrow = num_comp, ncol = 2, TRUE),
  prior_EX_tau_mean_comp = abind(matrix(log(  c(0.25, 0.125)), nrow = num_comp, ncol = 2, TRUE),
                                 matrix(log(2*c(0.25, 0.125)), nrow = num_comp, ncol = 2, TRUE),
                                 along = 0),
  prior_EX_tau_sd_comp = abind(matrix(log(4) / 1.96, nrow = num_comp, ncol = 2, TRUE),
                               matrix(log(4) / 1.96, nrow = num_comp, ncol = 2, TRUE),
                               along = 0),
  prior_EX_mu_mean_inter = rep(0, num_inter),
  prior_EX_mu_sd_inter = rep(sqrt(2) / 2, num_inter),
  prior_EX_tau_mean_inter = matrix(log(0.25), nrow = num_strata, ncol = num_inter),
  prior_EX_tau_sd_inter = matrix(log(2) / 1.96, nrow = num_strata, ncol = num_inter),
  prior_EX_prob_comp = matrix(0.9, nrow = num_groups, ncol = num_comp),
  prior_EX_prob_inter = matrix(1.0, nrow = num_groups, ncol = num_inter),
  prior_is_EXNEX_comp = rep(TRUE, num_comp),
  prior_is_EXNEX_inter = rep(FALSE, num_inter),
  prior_tau_dist = 1,
  prior_PD = FALSE
)
## Recover user set sampling defaults
options(.user_mc_options)

OncoBayes2 documentation built on July 26, 2023, 5:30 p.m.