devel/dual2.R

In 0liver0815/onc-crmpack-test: Object-Oriented Implementation of CRM Designs

#####################################################################################
## Author: Daniel Sabanes Bove [sabanesd *a*t* roche *.* com]
## Project: Object-oriented implementation of CRM designs
##
## Time-stamp: <[dual.R] by DSB Son 11/01/2015 14:55>
##
## Description:
## Test the dual endpoint stuff. For development only!!
##
## History:
## 24/03/2014   file creation
## 22/12/2014   test the new JAGS implementation
## 08/05/2018   version to test package directly on convergence/extrapolation
###################################################################################

library(crmPack)

## set up the model
model <- DualEndpointRW(mu=c(0, 1),
                        Sigma=matrix(c(1, 0, 0, 1), nrow=2),
                        sigma2betaW=
                        0.01,
                        ## c(a=20, b=50), ## gives very unstable results!!
                        sigma2W=
                        c(a=0.1, b=0.1),
                        rho=
                        c(a=1, b=1),
                        ## c(a=20, b=10)
                        smooth="RW1")

data <- DataDual(
            c(0.1, 0.5, 1.5, 3, 6, 10, 10, 10,
              20, 20, 20, 40, 40, 40, 50, 50, 50),
            y=
            as.integer(c(0, 0, 0, 0, 0, 0, 1, 0,
                         0, 1, 1, 0, 0, 1, 0, 1, 1)),
            w=
            c(0.3, 0.4, 0.5, 0.4, 0.6, 0.7, 0.5, 0.6,
              0.5, 0.5, 0.55, 0.4, 0.41, 0.39, 0.3, 0.3, 0.2),
            doseGrid=
            c(0.1, 0.5, 1.5, 3, 6,
              seq(from=10, to=80, by=2)))
data
data@nGrid
data@nObs

options <- McmcOptions(burnin=10000,
               step=2,
               samples=50000)


samples <- mcmc(data, model, options, verbose=TRUE)

str(samples)

plot(samples@data$betaW[, 40], type="l")
plot(samples@data$betaW[, 30], type="l")
## convergence is obtained both for RW1 and RW2 - good

plot(samples, model, data)
plot(samples, model, data, extrapolate=FALSE)