Package index • adnuts

All functions

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
.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
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_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
sample_nuts() sample_rwm(): Bayesian inference of an ADMB model using the no-U-turn sampler (NUTS) or random walk Metropolis (RWM) algorithms.