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CodeArchitecture
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. One can also invoke help arStruct
for additional information. 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.
An important feature of the D2D framework is the ability of Profile Likelihood Estimations (PLE). An existing ar
struct (see above) can be used to initialise ar.ple
. Results of ple
can be loaded, saved, plotted and reported separately with respective commands.
- 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?