SimRMD: Simulate trial characters of the phase I dose-finding design.
In phase1RMD: Repeated Measurement Design for Phase I Clinical Trial

Description Usage Arguments Details Value Examples

SimRMD uses the design parameters to simulate the trial characters of phase I dose-finding design.

SimRMD(seed=2014, strDose=1, chSize=3, trlSize=36,
   numTrials=1000, sdose=1:6, MaxCycle=6, tox.target=0.28,
   control, iter=10000, burnin=4000, thin=1, chains=1,    
   pathout='./', tox.matrix, wm = matrix(c(0, 0.5, 0.75, 1  , 1.5, 
                                        0, 0.5, 0.75, 1  , 1.5, 
                                        0, 0  , 0   , 0.5, 1  ), 
                                        byrow = T, ncol = 5), toxmax = 2.5)

`seed`	Random seed of the simulation (default = 2014).
`strDose`	Start dose (default = 1).
`chSize`	Size of each patient cohort (default = 3).
`trlSize`	Total number of patients in the trial (default = 36).
`numTrials`	Number of simulated trials (default = 1000).
`sdose`	Dose range (default = 1:6).
`MaxCycle`	Maximum treatment cycle (default = 6).
`tox.target`	Target toxicity score (default = 0.28).
`control`	Prior distributions as specified by `parm` function.
`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).
`pathout`	The output directory of simulation results (default = './').
`tox.matrix`	Four-dimension array contains Dose, Cycle, Toxicity Type, Toxicity Grade.
`wm`	Clinical weight matrix, where toxicity types define the rows while the toxicity grades define the columns. Usually solicited from physicians.
`toxmax`	The normalization constant used in computing nTTP score. For details, see Ezzalfani et al(2013).

The SimRMD 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.

A list containing the following elements:

`DOSE-RECOMMENDED`	Recommended dose for the next patient cohort.
`Estimate`	Mean, SD, and median estimates of the toxicity score at each dose level.
`Quantiles`	2.5%, 25%, 50%, 75%, 97.5% quantile estimates of the toxicity score at each dose level.

# 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)
 )


# Generate the toxicity matrix
# tox.matrix <- GenToxProb(
#    toxtype = c("Renal", "Neuro", "Heme"), 
#	intercept.alpha = c(2, 3, 4.2, 5.7), 
#	coef.beta = c(-0.2, -0.4, -0.7), 
#	cycle.gamma = 0)

# Simulate the dose-recommendation based on the toxicity matrix
# simu <- SimRMD(seed=2014, strDose=1, chSize=3, trlSize=12,
#    numTrials=1, sdose=1:6, MaxCycle=5, tox.target=0.28,
#    control=control, iter=10, burnin=2, thin=1, chains=1,    
#    pathout='./', tox.matrix=tox.matrix)