SimEfftoxUt: Simulates trial replications from the Efftox model with...

In Phase12Compare: Simulates SPSO and Efftox Phase 12 Trials with Correlated Outcomes

Description

Simulates replications from a Bayesian adaptive phase 12 clinical trial design using the Efftox model and a optimality function based on mean utility. Does not assign patient cohorts to unacceptably toxic or inefficous dose levels.

Usage

SimEfftoxUt(
  NSims,
  Dose,
  PE,
  PT,
  corET,
  Nmax,
  cohort,
  UT,
  CutE,
  CutT,
  AcceptE,
  AcceptT,
  HypermeansEFF,
  HypervarsEFF
)

Arguments

NSims	Number of trial simulations to run.
Dose	Logarithm of raw dose levels - the average logarithm of the raw dose levels.
PE	True efficacy probability for each dose.
PT	True toxicity probaiblity for each dose.
corET	Correlation parameter between efficacy and toxicity probability.
Nmax	Maximum trial sample size.
cohort	Patient cohort size.
UT	Utility matrix for the four bivariate (efficacy, toxicity) events.
CutE	Cutoff for efficacy probability acceptability. Dose-efficacy probabilities must be larger than this for patient assignment.
CutT	Cutoff for toxicity probability acceptability. Dose-toxicity probabilities must be smaller than this for patient assignment.
AcceptE	Posterior probability threshold for efficacy acceptability.
AcceptT	Posterior probability threshold for toxicity acceptability.
HypermeansEFF	Hypermeans for the Efftox model. In order, entries are hypermeans for (beta_0,E,beta_1,E,beta_2,E,beta_0,T,beta_1,T,psi).
HypervarsEFF	Hypervariances for the Efftox model. In order, entries are hypervariances for (beta_0,E,beta_1,E,beta_2,E,beta_0,T,beta_1,T,psi).

Value

A list with the first entry corresponding to a matrix with: (1) True toxicity probabilities at each dose, (2) True efficacy probabilities at each dose, (3) True mean utility of each dose, (4) Optimal dose selection probability, (5) Average sample size of patients treated at each dose. The second entry of the list contains a vector with rows corresponding to (1) the true binary bivariate correlation between efficacy and toxicity, (2) Stopping probability of the trial, (3) Average number of efficacy events, (4) Average number of toxicity events, and (5) Delta.

Examples

library(mvtnorm)
##True toxicity probability
PT=c(.05,.10,.15,.20,.30)
##True Efficacy Probability
PE=c(.2,.4,.6,.65,.7)
#True Correlation
corET=.5
##Number of simulations
NSims=1 ##Increase this when using
##Hypermeans and hypervariances
HypermeansEFF = c(.022,3.45,0,-4.23,3.1,0)
HypervarsEFF = c(2.6761, 2.6852, .2, 3.1304, 3.1165, 1)
HypervarsEFF=HypervarsEFF^2
##Trial Parameters
##Cohort Size, N^F and N_ET
cohort=3
##Starting Dose
DoseStart=1
##Vector of Numerical Doses
Dose = c(1,2,3,3.5,5)
##Dose for Eff-Tox
Dose=log(Dose)-mean(log(Dose))
Nmax=30 ##Max Sample Size
#Acceptability Criterion
CutE=.3
CutT=.4
##Limits on acceptability
AcceptE=.1
AcceptT=.1
##UTILITY Matrix
UT = matrix(c(38.23529,100,0,61.76471),nrow=2,byrow=TRUE)
RESULTS=SimEfftoxUt(NSims, Dose,PE,  PT, corET,
Nmax, cohort, UT, CutE, CutT, AcceptE,AcceptT,  HypermeansEFF, HypervarsEFF)
RESULTS

Phase12Compare documentation built on July 31, 2020, 5:07 p.m.