calc_decision_rules: Calculate a decision rule table for interim monitoring of a...

Description Usage Arguments Value Examples

View source: R/calc_decision_rules.R

Description

This function will take the posterior and predictive thresholds for a pre-specified design with a given null response rate and fixed interim looks and total sample size, and return the decision rules at each interim analysis and the end of the trial. Intended for use after selecting an optimal design using the functions calibrate_thresholds and optimize_design.

Usage

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calc_decision_rules(
  n,
  N,
  theta,
  ppp,
  p0,
  direction = "greater",
  delta = NULL,
  prior = c(0.5, 0.5),
  S = 5000
)

Arguments

n

matrix containing the total number of patients accrued so far at each interim look in the standard of care (column 1) and experimental (column 2) arms for two-sample case; vector of sample size accrued so far at each interim look for one-sample case. The last value should be equal to the total sample size at the end of the trial. If only a single look will be done at the end of the trial, this can be a vector specifying the total sample size c(N0, N1) for the two-sample case or an integer specifying the total sample size N for the one-sample case

N

the total planned sample size at the end of the trial, c(N0, N1) for two-sample case; integer of total planned sample size at end of trial N for one-sample case

theta

The target posterior probability. e.g. Efficacy decision if P(p1 > p0) > theta for the two-sample case with greater direction.

ppp

The target predictive probability. e.g. Stop the trial if the predictive probability falls below this target.

p0

The target value to compare to in the one-sample case. Set to NULL for the two-sample case.

direction

"greater" (default) if interest is in P(p1 > p0) and "less" if interest is in P(p1 < p0) for two-sample case. For one-sample case, "greater" if interest is in P(p > p0) and "less" if interest is in P(p < p0).

delta

clinically meaningful difference between groups. Typically 0 for two-sample case. NULL for one-sample case (default).

prior

hyperparameters of prior beta distribution. Beta(0.5, 0.5) is default

S

number of samples, default is 5000

Value

In the one-sample case, returns a tibble with n at each look, r at each look, and ppp, the associated posterior predictive probability. Stop the trial at that look if the number of observed responses is <=r. At the end of the trial, the treatment is considered promising if the number of observed responses is >r. In the two-sample case, returns a tibble with n0 and n1, the number enrolled subjects in the control and experimental arms at each look, respectively, r0 and r1, the number of possible responses in the control and experimental arms at each look, respectively, and ppp, the associated posterior predictive probability. Any NA value in either table represents an interim look where there is no number of responses that would lead to stopping the trial.

Examples

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set.seed(123)

# One-sample case
calc_decision_rules(n = seq(5, 25, 5), N = 25, theta = 0.86, ppp = 0.2, p0 = 0.1)

# Two-sample case
calc_decision_rules(n = cbind(seq(5, 25, 5), seq(5, 25, 5)), N = c(25, 25),
theta = 0.86, ppp = 0.2, p0 = NULL, direction = "greater", delta = 0,
prior = c(0.5, 0.5), S = 5000)

ppseq documentation built on Sept. 9, 2021, 9:06 a.m.