No-U-Turn MCMC Sampling for 'ADMB' Models

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Documentation for package ‘adnuts’ version 1.1.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

.check_ADMB_version	Check that the model is compiled with the right version of ADMB which is 12.0 or later
.check_console_printing	Check if the session is interactive or Rstudio which has implications for parallel output
.check_model_path	Check that the file can be found
.getADMBHessian	Read in admodel.hes file
.sample_admb	Hidden wrapper function for sampling from ADMB models
.update_model	Convert model name depending on system
adfit	Constructor for the "adfit" (A-D fit) class
adnuts	adnuts: No-U-turn sampling for AD Model Builder (ADMB)
as.data.frame.adfit	Convert object of class adfit to data.frame. Calls 'extract_samples'
check_identifiable	Check identifiability from model Hessian
extract_sampler_params	Extract sampler parameters from a fit.
extract_samples	Extract posterior samples from a model fit.
is.adfit	Check object of class adfit
launch_shinyadmb	Launch shinystan for an ADMB fit.
launch_shinytmb	Launch shinystan for a TMB fit.
pairs_admb	Plot pairwise parameter posteriors and optionally the MLE points and confidence ellipses.
plot.adfit	Plot object of class adfit
plot_marginals	Plot marginal distributions for a fitted model
plot_sampler_params	Plot adaptation metrics for a fitted model.
plot_uncertainties	Plot MLE vs MCMC marginal standard deviations for each parameter
print.adfit	Print summary of adfit object
sample_admb	Deprecated version of wrapper function. Use sample_nuts or sample_rwm instead.
sample_inits	Function to generate random initial values from a previous fit using adnuts
sample_nuts	Bayesian inference of an ADMB model using the no-U-turn sampler (NUTS) or random walk Metropolis (RWM) algorithms.
sample_rwm	Bayesian inference of an ADMB model using the no-U-turn sampler (NUTS) or random walk Metropolis (RWM) algorithms.
sample_tmb	Bayesian inference of a TMB model using the no-U-turn sampler.
sample_tmb_hmc	Draw MCMC samples from a model posterior using a static HMC sampler.
sample_tmb_nuts	Draw MCMC samples from a model posterior using the No-U-Turn (NUTS) sampler with dual averaging.
sample_tmb_rwm	[Deprecated] Draw MCMC samples from a model posterior using a Random Walk Metropolis (RWM) sampler.
summary.adfit	Print summary of object of class adfit
wrappers	Bayesian inference of an ADMB model using the no-U-turn sampler (NUTS) or random walk Metropolis (RWM) algorithms.