get_all_params: Extract all model parameters from the PopED database.

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

Extract all model parameters from the PopED database.

Description

Extract all model parameters from the PopED database.

Usage

get_all_params(poped.db)

Arguments

poped.db

A PopED database.

Value

A list containing:

bpop	A vector of fixed effect parameter values.
d	A vector of between subject variability parameters
covd	A vector of the covariances of the between subject variability parameters. Row major format of the lower triangular portion of the D (OMEGA) matrix
docc	A vector of the between occasion variability (BOV) terms in the model
covdocc	A vector of the covariances between the BOV terms. Row major of the lower triangular portion of the BOV matrix.
sigma	A vector of the residual unexplained variances (RUV)
covsigma	A vector of the covariances between the RUV terms
all	A vector with all of the above, in the order of this list.

Examples

library(PopED)

############# START #################
## Create PopED database
## (warfarin example)
#####################################

## Warfarin example from software comparison in:
## Nyberg et al., "Methods and software tools for design evaluation 
##   for population pharmacokinetics-pharmacodynamics studies", 
##   Br. J. Clin. Pharm., 2014. 

## find the parameters that are needed to define from the structural model
ff.PK.1.comp.oral.sd.CL

## -- parameter definition function 
## -- names match parameters in function ff
sfg <- function(x,a,bpop,b,bocc){
  parameters=c(CL=bpop[1]*exp(b[1]),
               V=bpop[2]*exp(b[2]),
               KA=bpop[3]*exp(b[3]),
               Favail=bpop[4],
               DOSE=a[1])
  return(parameters) 
}

## -- Define model, parameters, initial design
poped.db <- create.poped.database(ff_fun=ff.PK.1.comp.oral.sd.CL,
                                  fg_fun=sfg,
                                  fError_fun=feps.prop,
                                  bpop=c(CL=0.15, V=8, KA=1.0, Favail=1), 
                                  notfixed_bpop=c(1,1,1,0),
                                  d=c(CL=0.07, V=0.02, KA=0.6), 
                                  sigma=c(prop=0.01),
                                  groupsize=32,
                                  xt=c( 0.5,1,2,6,24,36,72,120),
                                  a=c(DOSE=70))

############# END ###################
## Create PopED database
## (warfarin example)
#####################################


get_all_params(poped.db)

andrewhooker/PopED documentation built on Nov. 23, 2023, 1:37 a.m.