expo3-nonmem-bayes

This repository contains examples of the various tasks associated with the completion of a modeling project with Bayesian estimation in NONMEM. The goal is to represent the most up-to-date packages and methodologies for completing these tasks. These will evolve with time so check back periodically. be best to check back periodically.

Data

• PK model estimation data set
  • location : data/derived/pk.csv
  • spec file : data/derived/pk.yml

Scripts

• Model creation, submission & management: model-management.R
  • Example code that may be used in model-management.R: model-management-demo.Rmd
• Diagnostic plots are created in: model-diagnostics.R
  • this R script uses Rmd templates to make html files that will be saved to your model directory:
    • diagnostic-templates > template-model-bayes.Rmd
    • diagnostic-templates > template-mcmc.Rmd
• Model summary: model-summary.Rmd
• Parameter tables:
  • Parameter key for all tables is included in a yaml: pk-parameter-key.yaml
  • Parameter table for base model: pk-base-model-table.R
  • Parameter table for final model (incl. covariates): pk-final-model-table.R
• Figures for report
  • Goodness-of-fit evaluations from model-diagnostics.R with template-model-bayes.Rmd
  • MCMC diagnostics from model-diagnostics.R with template-mcmc.Rmd
  • Covariate effects evaluation from forest-plots.R
• Visual predictive checks:
  • pk-vpc-final.R
  • pk-pcvpc-final.R

Helper functions

• Helper functions for model management: functions-model.R
• Helper functions for scripts creating tables: functions-tables.R
• Helper functions for creating the model diagnostics: functions-diagnostics.R
• Helper functions for various Bayesian-specific diagnostics: functions-mcmc-diagnostics.R and functions-diagnostics-rhat-ess.R

Metworx Version

• metworx-22-09.00.03

R Version

• 4.1.3

NONMEM Version

• 7.5.1

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