Technical Appendix
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Adding a technical appendix for advanced users and interested contributors to the Manual. This is something we'll need to update as Torsten evolves. I finished writing the first version (for release 0.83). Different sections will be suited for different readers.
The organization is as follows:
.Preface (with a quote by Torsten!)
A. Bayesian Data Analysis with Stan
A.1 Hamiltonian Monte Carlo
A.2 Automatic Differentiation
B. Ordinary Differential Equations in Pharmacometrics
B.1 When do ODEs arise?
B.2 An Example: the Two Compartment Model
B.3 Overview of Tools to Solve Differential Equations
B.4 The Event Schedule
B.4.1 Handling Exterior Interventions
B.4.2 Dosing Events
B.4.3 Model Parameters
C. Solving Ordinary Differential Equations
C.1 Analytical Solution
C.2 The Matrix Exponential
C.3 Numerical Integrators
C.3.1 Nonstiff and stiff systems
C.3.2 Jacobian of the solution
C.4 Mixed Solver
C.5 Rates
C.6 Steady State Solution
C.6.1 Algebraic Solver
D. Code Implementation of Torsten