No-U-Turn MCMC Sampling for 'ADMB' Models
Constructor for the "adfit" (A-D fit) class
adnuts: No-U-turn sampling for AD Model Builder (ADMB)
Convert object of class adfit to data.frame. Calls extract_samples
Check identifiability from model Hessian
Check that the model is compiled with the right version of ADMB which ...
Check if the session is interactive or Rstudio which has implications ...
Check that the file can be found
Read in admodel.hes file
Hidden wrapper function for sampling from ADMB models
Convert model name depending on system
Extract sampler parameters from a fit.
Extract posterior samples from a model fit.
Check object of class adfit
Launch shinystan for an ADMB fit.
Launch shinystan for a TMB fit.
Plot pairwise parameter posteriors and optionally the MLE points and c...
Plot object of class adfit
Plot marginal distributions for a fitted model
Plot adaptation metrics for a fitted model.
Plot MLE vs MCMC marginal standard deviations for each parameter
Print summary of adfit object
Deprecated version of wrapper function. Use sample_nuts or sample_rwm ...
Function to generate random initial values from a previous fit using a...
Bayesian inference of a TMB model using the no-U-turn sampler.
Draw MCMC samples from a model posterior using a static HMC sampler.
Draw MCMC samples from a model posterior using the No-U-Turn (NUTS) sa...
[Deprecated] Draw MCMC samples from a model posterior using a Random W...
Print summary of object of class adfit
Bayesian inference of an ADMB model using the no-U-turn sampler (NUTS)...
Bayesian inference using the no-U-turn (NUTS) algorithm by Hoffman and Gelman (2014) <https://www.jmlr.org/papers/v15/hoffman14a.html>. Designed for 'AD Model Builder' ('ADMB') models, or when R functions for log-density and log-density gradient are available, such as 'Template Model Builder' models and other special cases. Functionality is similar to 'Stan', and the 'rstan' and 'shinystan' packages are used for diagnostics and inference.
Useful links