RunRMD: Toxicity-based Dose estimation for the next patient cohort.

In phase1RMD: Repeated Measurement Design for Phase I Clinical Trial

Description

RunRMD estimate the dosage for the next patient cohort using TTP measured multidimensional toxicity data collected from multiple treatemnt cycles of the existing patients.

Usage

  RunRMD(data, control, trlSize = 36, tox.target = 0.28, 
  sdose = 1:6, strDose = 1, iter=10000, burnin=4000, thin=1, chains=1)

Arguments

data	Toxicty data collected from the multiple treatment cycles of existing patient cohorts.
control	Prior distributions as specified by parm function.
trlSize	Total number of patients in the trial.
tox.target	Target toxicity score (default = 0.28).
sdose	Total number of patients in the trial.
strDose	Start dose.
iter	Total number of MCMC simulations (default = 4000).
burnin	Number of burn-ins in the MCMC simulation (default = 1000).
thin	Thinning parameter (default = 1).
chains	Number of chains in the MCMC simulation (default = 1).

Details

The RunRMD function uses the patient data structure patdata to fit the linear mixed model as specified by formula based on the prior distributions as specified by control. The parameters of the MCMC simulation are specified by iter: the number of iterations, burnin: burn-ins, thin: thinning parameter and chains: number of chains in the MCMC simulation. The target nTTP score is defined by tox.target, default = 0.28.

Value

A list containing the following elements:

nxtdose	Recommended dose for the next patient cohort.
tox.est	Mean, SD, median estimates and 2.5%, 25%, 50%, 75%, 97.5% quantile estimates of the toxicity score at each dose level.

Examples

# Setup the prior distributions for the phase I dose-finding model:
control <- list(
 beta.dose = parm("normal", mean = 0, var = 1000),
 beta.other = parm("normal", mean = 0, var = 1000 ),
 gamma = parm("normal", mean = 0, var = 100 ),
 s2.gamma = parm("invgamma", shape = 0.001, scale = 0.001),
 s2.epsilon = parm("invgamma", shape = 0.001, scale = 0.001)
 )
 
# Load the example patient toxicity data:
# data(patdata)

# Estimate the dose-recommendation of the next patient cohort based on the toxicity data:
# fit <- RunRMD(data = patdata, control = control, trlSize = 36, tox.target = 0.28, 
#  sdose = 1:6, strDose = 1, iter = 2000, burnin = 500, thin = 1, chains = 1)
  

phase1RMD documentation built on March 13, 2020, 1:40 a.m.