phase1RMD (version 1.0.9)

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

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).

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.

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.

Examples

# NOT RUN {
# 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)
  
# }