-
Notifications
You must be signed in to change notification settings - Fork 28
MCMC Methods and Functions
MCMC functions are stored in folder .../arFramework3/MCMC/
They include:
-
arMC3 - MCMC sampler with covariance adaptation and exchange methods for multiple chains. The corresponding options are stored in ar.mc3
-
arPlotMCMCChains - Plot MCMC Chains
-
arPlotMarginalized - Plot MCMC histograms
-
arPlotPLEComparisonToMCMC - Plot MCMC histograms and ple runs together to compare histograms to profiles. Please ple profiles before running this function.
-
arPlotCorrelations - Plot 2D correlation structure of parameters including histograms
-
arGeweke - Run Geweke convergence test on parameter sample
-
arGewekePlot - Plot results of successive Geweke tests using different fractions of chain
-
arGelmanRubinBrooks - Run Gelman Rubin Brooks convergence/similarity test on two parameter samples (runs)
- 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?