get_efftox_priors: Get normal prior hyperparameters for the EffTox model.

In trialr: Clinical Trial Designs in 'rstan'

Get normal prior hyperparameters for the EffTox model.

Description

Get normal prior hyperparameters for the EffTox model using the algorithm presented in Thall et al. (2014) that targets a family of priors with a pre-specified effective sample size (ESS).

Usage

get_efftox_priors(
  doses = NULL,
  scaled_doses = NULL,
  pi_T,
  ess_T,
  pi_E,
  ess_E,
  num_samples = 10^4,
  seed = 123
)

Arguments

doses	A vector of numbers, the doses under investigation. They should be ordered from lowest to highest and be in consistent units. E.g. to conduct a dose-finding trial of doses 10mg, 20mg and 50mg, use c(10, 20, 50). Specify doses or scaled_doses.
scaled_doses	Optional, vector of numbers, representing the scaled doses under investigation. Thall et al. advocate scaled_doses = log(doses) - mean(log(doses)), and that is what we use here. Specify doses or scaled_doses.
pi_T	Vector of prior expectations of probabilities of toxicity at the doses. Should be congruent to doses or scaled_doses.
ess_T	Numerical, sought total effective sample size for priors on parameters in the toxicity sub-model. Thall et al. (2014) advocate values in (0.3, 1.0) but stress that stress-testing with values outside this range may be necessary.
pi_E	Vector of prior expectations of probabilities of efficacy at the doses. Should be congruent to doses or scaled_doses.
ess_E	Numerical, sought total effective sample size for priors on parameters in the efficacy sub-model. Thall et al. (2014) advocate values in (0.3, 1.0) but stress that stress-testing with values outside this range may be necessary.
num_samples	Number of samples to draw from priors. The default 10^4 seems to be a nice compromise between accuracy and speed. Orders of magnitude larger take a long time to run.
seed	Optional seed. This process involves randomness so seeds are used for repeatable results.

Value

An instance of class efftox_priors.

References

Thall, P., Herrick, R., Nguyen, H., Venier, J., & Norris, J. (2014). Effective sample size for computing prior hyperparameters in Bayesian phase I-II dose-finding. Clinical Trials, 11(6), 657-666. https://doi.org/10.1177/1740774514547397

Examples

## Not run: 
# Reproduce the priors calculated in Thall et al. (2014)
p <- get_efftox_priors(
  doses = c(1.0, 2.0, 4.0, 6.6, 10.0),
  pi_T = c(0.02, 0.04, 0.06, 0.08, 0.10), ess_T = 0.9,
  pi_E = c(0.2, 0.4, 0.6, 0.8, 0.9), ess_E = 0.9
)
p
# These are close to the published example. They do not match exactly because
# the process of deriving them is iterative.

## End(Not run)

trialr documentation built on April 1, 2023, 12:03 a.m.