RunAdaptiveEffToxTrial {Phase123}

Simulates repitions of an Adaptive Eff-Tox Trial.

Description

This function simulates repititions of an adaptive Eff-Tox Trial and returns a list containing the optimal dose chosen

Usage

RunAdaptiveEffToxTrial(DoseStart, Dose, Hypermeans, Hypervars, Contour,
  PiLim, ProbLim, cohort, NET, NF, B, nSims, PETrue, PTTrue)

Arguments

DoseStart

Dose to start enrolling cohorts of patients at.

Dose

Vector containing the standardized doses considered.

Hypermeans

Vector containing prior hypermeans of length 6 for Eff-Tox parameters.

Hypervars

Vector containing prior hypervariances of length 6 for Eff-Tox parameters.

Contour

Vector containing 4 entries used to make the desireability function. Contour[1] contains a desired toxicity probability given efficacy, Countour[2] contains a desired efficacy probability given toxicity, and (Contour[3],Contour[4]) is an equally desireable pair of efficacy and toxicity probabilities that are non-zero or one.

PiLim

Vector of length two with PiLim[1] containing the acceptable lower limit on efficacy probability and PiLim[2] containing the acceptable upper limit on toxicity probability.

ProbLim

Vector of length two with ProbLim[1] containing the probability cutoff for acceptable efficacy probability and ProbLim[2] containing the probability cutoff for acceptable toxicity probability.

cohort

Size of each patient cohort.

NET

Maximum sample size for phase I/II.

NF

Number of patients to assign optimal doses prior to adaptive randomization.

B

Number of iterations to perform in the MCMC.

nSims

Number of simulated trials to run.

PETrue

True vector of efficacy probabilities for each dose.

PTTrue

True vector of toxicity probabilities for each dose.

Value

List containing the vector of optimal doses chosen, a matrix of posterior desireability scores for each trial, and a matrix consisting of patient dose assignments and Toxicity and Efficacy indicators, with each Nmax rows corresponding to a separate trial. Trials that are stopped due to excessive toxicity probabilty or small efficacy probabilities are not included in the final results.

Examples

##Doses, YE,YT
##Starting Dose
DoseStart=1
##Vector of Numerical Doses
Dose = c(1,2,3,3.5,5)
Dose=(Dose-mean(Dose))/sd(Dose)
## Contour Vector
Contour = c(.35, .75,.7,.4)
##Hypermeans
Hypermeans = c(.022,3.45,0,-4.23,3.1,0)
Hypervars = c(2.6761, 2.6852, .2, 3.1304, 3.1165, 1)
Hypervars=Hypervars^2
##Acceptability Criteria
PiLim = c(.3,.4)
ProbLim=c(.1,.1)
##Cohort Size, N^F and N_ET
cohort=3
NF=15
NET=30
PTTrue = c(.1,.15,.25,.35,.5)
PETrue=c(.2,.4,.6,.65,.7)
##Number of iterations for MCMC
B=2000
### Number of Simulations
nSims=1
RunAdaptiveEffToxTrial(DoseStart,Dose, Hypermeans,  Hypervars,
Contour, PiLim, ProbLim,  cohort, NET,  NF, B, nSims, PETrue, PTTrue )