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CodeArchitecture
ladlung edited this page May 21, 2015
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Architecture of the code and the most important commands of the D2D framework. After initialization with arInit
, model and data files can be loaded. The latter ones are allowed in various formats. The command arCompileAll
links all model and data files under the various conditions and creates C code. The central ar
struct is created. For further information on the ar
struct, click here. Simulation and parameter estimations are performed under MATLAB. Obtained results can be visualised with arPlot
. Results can be saved and loaded from a workspace.mat
file and presentations and reports can be created automatically created for documentation. A more detailed overview over important commands can be found here.
- Installation and system requirements
- Setting up models
- First steps
- Advanced events and pre-equilibration
- Computation of integration-based prediction bands
- How is the architecture of the code and the most important commands?
- What are the most important fields of the global variable ar?
- What are the most important functions?
- Optimization algorithms available in the d2d-framework
- Objective function, likelhood and chi-square in the d2d framework
- How to set up priors?
- How to set up steady state constraints?
- How do I restart the solver upon a step input?
- How to deal with integrator tolerances?
- How to implement a bolus injection?
- How to implement washing and an injection?
- How to implement a moment ODE model?
- How to run PLE calculations on a Cluster?