hist_SA: Single-agent example

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

Single-agent example

Description

Example data from the application in Neuenschwander, et. al. 2008, from an "open-label, multicenter, non-comparative, dose-escalation cancer trial to characterize the safety, tolerability, and pharmacokinetic profile of a drug and to determine its MTD."

Usage

hist_SA

Format

A data frame with 5 rows and 4 variables:

group_id

study

drug_A

dose

num_patients

number of patients

num_toxicities

number of events

References

Neuenschwander, B., Branson, M., & Gsponer, T. (2008). Critical aspects of the Bayesian approach to phase I cancer trials. Statistics in medicine, 27(13), 2420-2439.

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 from Neuenschwander, B., et al. (2009). Stats in Medicine

dref <- 50

## Since there is no prior information the hierarchical model
## is not used in this example by setting tau to (almost) 0.
blrmfit <- blrm_exnex(
  cbind(num_toxicities, num_patients - num_toxicities) ~
      1 + log(drug_A / dref) |
      0 |
      group_id,
  data = hist_SA,
  prior_EX_mu_comp = mixmvnorm(c(1, logit(1 / 2), log(1), diag(c(2^2, 1)))),
  ## Setting prior_tau_dist=NULL disables the hierarchical prior which is
  ## not required in this example as we analyze a single trial.
  prior_tau_dist = NULL,
  prior_PD = FALSE
)
## Recover user set sampling defaults
options(.user_mc_options)

OncoBayes2 documentation built on April 11, 2025, 5:42 p.m.