trialr (version 0.0.7)

efftox_simulate: Run EffTox simulations

Description

Run EffTox simulations for assumed true efficacy and toxicity curves.

Usage

efftox_simulate(dat, num_sims, first_dose, true_eff, true_tox, cohort_sizes,
  ...)

Arguments

dat

An instance of efftox_params, a list of EffTox parameters. An example is yielded by efftox_parameters_demo.

num_sims

integer, number of simulated iterations

first_dose

integer, the dose-level to give to patient 1, e.g. 1 for the lowest dose.

true_eff

the true probabilities of efficacy at the doses under investigation; a vector of numbers between 0 and 1.

true_tox

the true probabilities of toxicity at the doses under investigation; a vector of numbers between 0 and 1.

cohort_sizes

a vector of integer cohort sizes. A dose decision is made when each cohort is completed and the next cohort is treated at the recommended dose. To conduct a trial using at most 20 patients, where dose is re-evaluated after every second patient, use rep(2, 10). To conduct a trial of 8 patients where dose is re-evaluated after each single patient, use rep(1, 8). Cohort size need not be uniform. E.g. c(rep(1, 5), rep(3, 10)) represents a trial where the dose is re-evaluated after each patient for the first 5 patients, and then after every third patient for a further 30 patients.

...

Extra parameters provided via the ellipsis are passed to stan::sampling

Value

A list with named elements recommended_dose, efficacies, toxicities, and doses_given.

Examples

# NOT RUN {
dat <- efftox_parameters_demo()
set.seed(123)
# Let's say we want to use only 2 chains. Extra args are passed to stan
# }
# NOT RUN {
sims <- efftox_simulate(dat, num_sims = 10, first_dose = 1,
                        true_eff = c(0.20, 0.40, 0.60, 0.80, 0.90),
                        true_tox = c(0.05, 0.10, 0.15, 0.20, 0.40),
                        cohort_sizes = rep(3, 13),
                        chains = 2)
table(sims$recommended_dose) / length(sims$recommended_dose)
table(unlist(sims$doses_given)) / length(unlist(sims$doses_given))
table(unlist(sims$doses_given)) / length(sims$recommended_dose)
# }
# NOT RUN {
# In real life, we would run thousands of iterations, not 10.
# This is an example.
# }