PK/PD Simulation

Usage

/simulate
/simulate rxode2
/simulate mrgsolve
/simulate <run_number>

What This Does

Scaffolds a PK/PD simulation workflow:

1. •Define or load model parameters (from NONMEM run or manual input)
2. •Set up dose scenarios
3. •Run population simulations with variability
4. •Generate spaghetti + median/PI plots
5. •Optionally propagate parameter uncertainty

Protocol

Step 1: Fetch Documentation

Use Context7 for the selected engine (rxode2 or mrgsolve).

Step 2: Determine Model Source

If $ARGUMENTS is a run number:

• •Load parameters from NONMEM output using xpose/aipharma
• •Translate NONMEM model structure to rxode2/mrgsolve syntax

If no run number:

• •Ask user for model structure and parameters
• •Or use a previously defined model file

Step 3: Define Dose Scenarios

Ask user for:

• •Dose levels and regimens
• •Number of subjects per scenario
• •Simulation duration
• •Special populations (if covariate effects included)

Step 4: Scaffold Report

Copy templates/simulation-report.qmd to reports/. Configure for selected engine and scenarios.

Step 5: Generate Simulations

• •Set set.seed() for reproducibility
• •Run N subjects per scenario (default: 1000)
• •Calculate median and 90% prediction intervals
• •Generate:
  • •Spaghetti plots (individual profiles)
  • •Median + PI ribbon plots
  • •Dose comparison overlays

Step 6: Review

• •Check no negative concentrations
• •Verify steady-state achieved if applicable
• •Compare to observed data if available

Non-Negotiables

• •set.seed() at top of every simulation script
• •Named parameter vectors (not positional)
• •Document all dose scenarios in header comments
• •dpi = 300 for all figures
• •Include parameter uncertainty propagation when bootstrap available