sample_par: Sample model parameters from a multivariate normal...

In amp.sim: Flexible Simulation Utilities for Pharmacometric Modeling

Sample model parameters from a multivariate normal distribution

Description

This function samples model parameters from NONMEMs covariate matrix (.cov) and final parameter estimates (.ext). Furthermore etas can also be sampled where eta blocks are taken into account (see details)

Usage

sample_par(
  ext,
  covmat = NULL,
  bootstrap = NULL,
  seed = NULL,
  nrepl = 10,
  inc_theta = TRUE,
  inc_eta = FALSE,
  verbose = FALSE,
  dropfixed = FALSE,
  uncert = FALSE,
  restheta = NULL
)

Arguments

ext	character string with location of ext file with final model parameters
covmat	character string with location of cov file with covariance matrix or data.frame of cov file
bootstrap	character string with location of ext files from bootrstrap or vector with ext files from bootstrap (relevant in case ext files should be excluded because of minimization issues)
seed	a numeric with the seed number used in set.seed to enable reproducibility, when not provided the seed from the global environment will be used (e.g. using base::set.seed)
nrepl	numeric with the number of replicates to sample
inc_theta	logical indicating if THETAs should be added to result
inc_eta	logical indicating if ETAs should be added to result
verbose	logical indicating if additional information should be added to result (e.g. OMEGA/SIGMA values)
dropfixed	logical indicating if parameters that are fixed should be dropped (can only be done in case covmat is provided)
uncert	logical indicating if the uncertainty should be sampled
restheta	character with the theta that describes residual error (e.g. "THETA3") in case uncertainty is sampled this parameter will be set to the population value

Details

In general the function can be used to sample from covariance matrix so the different parameters can be added to a simulation dataset or model to enable uncertainty simulations. In most cases it is not necessary to include OMEGAs or SIGMAs in these type of simulations. It can be convenient to add ETAs in the simulation dataset to perform a simulation where no $THETA or $OMEGA information is necessary. In case inc_eta is TRUE, the ETAs from the ext files are used and placed in a matrix to take into account covariance or 'BLOCKS'. A matrix from the ext file is constructed based on the naming of OMEGA values (e.g. OMEGA.2.1. will be added to row 2, column 1 and column 1, row 2). The matrix is used as Sigma for the mvrnorm function with mu=0.

Value

a dataframe with sampled values

Author(s)

Richard Hooijmaijers

See Also

MASS::mvrnorm

Examples

ext <- system.file("example_models","PK.1CMT.ORAL.COV.ext", package = "amp.sim")
cov <- system.file("example_models","PK.1CMT.ORAL.COV.cov", package = "amp.sim")
sample_par(ext, inc_eta = TRUE, nrepl = 5)
sample_par(ext, cov, uncert = TRUE, nrepl = 5)

amp.sim documentation built on May 7, 2026, 5:08 p.m.