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