inst/examples/ex.13.shrinkage.R

In andrewhooker/PopED: Population (and Individual) Optimal Experimental Design

library(PopED)

## following example 1.4.2 in PFIM
sfg <- function(x,a,bpop,b,bocc){
  ## -- parameter definition function 
  parameters=c(KA=bpop[1]*exp(b[1]),
               K=bpop[2]*exp(b[2]),
               V=bpop[3]*exp(b[3]),
               DOSE=a[1])
  return(parameters) 
}

ff <- function(model_switch,xt,parameters,poped.db){
  ##-- Model: One comp first order absorption
  with(as.list(parameters),{
    y<-(DOSE/V*KA/(KA-K)*(exp(-K*xt)-exp(-KA*xt)))
    return(list(y=y,poped.db=poped.db))
  })
}

## -- Residual unexplained variablity (RUV) function
## -- Additive + Proportional  
feps <- function(model_switch,xt,parameters,epsi,poped.db){
  returnArgs <- do.call(poped.db$model$ff_pointer,list(model_switch,xt,parameters,poped.db)) 
  f <- returnArgs[[1]]
  y = f + (0.5 + 0.15*f)*epsi[,1]
  
  return(list( y= y,poped.db =poped.db )) 
}

## -- Define initial design  and design space
poped.db <- create.poped.database(ff_fun=ff,
                                  fg_fun=sfg,
                                  fError_fun =feps,
                                  bpop=c(KA=2, K=0.25, V=15), 
                                  d=c(KA=1, V=0.25,0.1), 
                                  sigma=c(1),
                                  notfixed_sigma = c(0),
                                  groupsize=1,
                                  xt=c( 1,3,8),
                                  minxt=0,
                                  maxxt=10,
                                  a=100)


(shr_out <- shrinkage(poped.db))