trialr (version 0.1.6)

efftox_path_analysis: Fit an EffTox model to the incrementally observed outcomes on a trial pathway.

Description

Fit a EffTox model to the outcomes cumulatively observed at the end of each cohort in a trial pathway. E.g. if the trial pathway is 1EN 2NN 3BT, we have three cohorts of two patients. This function will fit the model to the following four states: before any patients have been evaluated; after 1EN; after 1EN 2NN; and finally after 1EN 2NN 3BT. This allows us to analyse how the trial model is evolving in its estimation as trial data is accumulated.

Usage

efftox_path_analysis(outcome_str, verbose = FALSE, ...)

Value

A list of dose_finding_path_node objects.

Arguments

outcome_str

A string representing the outcomes observed hitherto. See efftox_parse_outcomes for a description of syntax and examples. Alternatively, you may provide doses_given and tox parameters. See Details.

verbose

logical, TRUE to get log messages.

...

All other parameters are passed to stan_efftox.

Author

Kristian Brock

See Also

efftox_parse_outcomes, stan_efftox, dose_finding_path_node

Examples

if (FALSE) {
# EffTox example
paths <- efftox_path_analysis(
  outcome_str = '1NNN 2NEN 3NEB',
  real_doses = c(1.0, 2.0, 4.0, 6.6, 10.0),
  efficacy_hurdle = 0.5, toxicity_hurdle = 0.3,
  p_e = 0.1, p_t = 0.1,
  eff0 = 0.5, tox1 = 0.65,
  eff_star = 0.7, tox_star = 0.25,
  alpha_mean = -7.9593, alpha_sd = 3.5487,
  beta_mean = 1.5482, beta_sd = 3.5018,
  gamma_mean = 0.7367, gamma_sd = 2.5423,
  zeta_mean = 3.4181, zeta_sd = 2.4406,
  eta_mean = 0, eta_sd = 0.2,
  psi_mean = 0, psi_sd = 1, seed = 123, refresh = 0)

length(paths)  # 4
names(paths)[1]  # ""
names(paths)[2]  # "1NNN"
names(paths)[3]  # "1NNN 2NEN"
names(paths)[4]  # "1NNN 2NEN 3NEB"
# Each node is an analysis fit to the cumulative outcomes
# Converting to a tibble presents some nice tidyverse-related opportunities
library(tibble)
df <- as_tibble(paths)
df
}