sim.trials: Simulate full trial (both stages) x times

In iAdapt: Two-Stage Adaptive Dose-Finding Clinical Trial Design

Description

Results are displayed in a matrix format, where each row represents one trial simulation.

Usage

sim.trials(
  numsims,
  dose,
  dose.tox,
  p1,
  p2,
  K,
  coh.size,
  m,
  v,
  N,
  stop.rule = 9,
  cohort = 1,
  samedose = TRUE,
  nbb = 100
)

Arguments

numsims	number of simulated trials
dose	number of doses to be tested (scalar)
dose.tox	vector of true toxicities for each dose. Values range from 0 - 1.
p1	toxicity under null (unsafe DLT rate). Values range from 0 - 1.
p2	toxicity under alternative (safe DLT rate). Values range from 0 - 1; p1 > p2
K	threshold for LR. Takes integer values: 1,2,...(recommended K=2)
coh.size	cohort size (number of patients) per dose (Stage 1)
m	vector of mean efficacies per dose. Values range from 0 - 100. (e.g, T cell persistence - values b/w 5 and 80 per cent)
v	vector of efficacy variances per dose. Values range from 0 - 1. (e.g., 0.01)
N	total sample size for stages 1&2
stop.rule	if only dose 1 safe, allocate up to 9 (default) patients at dose 1 to collect more info.
cohort	cohort size (number of patients) per dose (Stage 2). Default is 1.
samedose	designates whether the next patient is allocated to the same dose as the previous patient. Default is TRUE. Function adjusts accordingly.
nbb	binomial parameter (default = 100 cells per patient)

Value

List of the following objects:

• sim.Y - estimated efficacy per each dose assignment

• sim.d - dose assignment for each patient in the trial

• safe.d - indicator of whether dose was declared safe

Examples

# Number of pre-specified dose levels
dose <- 5

# Vector of true toxicities associated with each dose
dose.tox <- c(0.05, 0.10, 0.20, 0.35, 0.45)       

# Acceptable (p_yes) and unacceptable (p_no) DLT rates used for establishing safety
p_no <- 0.40                                     
p_yes <- 0.15    

# Likelihood-ratio (LR) threshold
K <- 2                                          

# Cohort size used in stage 1
coh.size <- 3 

# Vector of true mean efficacies per dose (here mean percent persistence per dose)
m <- c(5, 15, 40, 65, 80)   # MUST BE THE SAME LENGTH AS dose.tox                  

# Efficacy(equal) variance per dose
v <- rep(0.01, 5) 

# Total sample size (stages 1&2)                            
N <- 25                                        

# Stopping rule: if dose 1 is the only safe dose, allocate up to 9 pts.
stop.rule <- 9 

sim.trials(numsims = 10, dose, dose.tox, p1 = p_no, p2 = p_yes, K, 
coh.size, m, v, N, stop.rule = stop.rule, cohort = 1, samedose = TRUE, nbb = 100)

iAdapt documentation built on Aug. 6, 2021, 9:08 a.m.