Introduction | Architecture | Workflow overview | Modeling datasets | Controller | Single-endpoint models | Controller creation | Models fitted with Monolix (versions 2016 and later) | Models fitted with NONMEM (versions 7.2 and later) | Models fitted with nlmixr | Optional arguments for controller creation | Multiple-endpoint models | Using pmx_endpoint() (only for Monolix) | A simplified syntax for endpoints (for Monolix, NONMEM and nlmixr) | Controller with covariates | Controller content | Plot names | Plot types | Default diagnostic plots | Visual Predictive Checks (VPC) | Initialization | VPC plot | Default | Scatter/Percentile | Binning | Stratification | Monolix-like customisation | Diagnostics report | Customizing plots | Visualization of BLQs (Monolix and NONMEM) | Simulated BLOQ (Monolix 2018 and later) | Customizing global settings - pmx_settings() | Remove DRAFT label globally | Use abbreviation definitions | Use finegrid.txt file for individual plots | Set stratification color legend | Define labels of categorical variables | Appendix | Generic Controller creation with pmx() | Software requirements | Monolix | NONMEM | nlmixr | Plots table | ggPMX main functions | ggPMX graphical parameters | Pre-defined configurations | Shrinkage | Default call | Var function | Shrinkage and stratification