# Fit Multivariate Response Generalized Additive Models using Hamiltonian Monte Carlo

## Documentation for package ‘bayesGAM’ version 0.0.2

- DESCRIPTION file.

## Help Pages

bayesGAM-package | The 'bayesGAM' package.
bayesGAM | 'bayesGAM' fits a variety of regression models using Hamiltonian Monte Carlo
bayesGAMfit | Contains results from 'rstan' as well as the design matrices and other data for the model.
bayesGAMfit-class | Contains results from 'rstan' as well as the design matrices and other data for the model.
bloodpressure | Blood pressure data from a clinical study
coef-method | Extract Model Coefficients
coefficients | Extract Model Coefficients
coefficients-method | Extract Model Coefficients
create_bivariate_design | Creates a design matrix from a bivariate smoothing algorithm
extract_log_lik_bgam | Extract the log likelihood from models fit by 'bayesGAM'
extract_log_lik_bgam-method | Extract the log likelihood from models fit by 'bayesGAM'
fitted | Extract fitted values from a model fit by 'bayesGAM'
fitted-method | Extract fitted values from a model fit by 'bayesGAM'
getDesign | Design matrices from a 'bayesGAMfit' object
getDesign-method | Design matrices from a 'bayesGAMfit' object
getModelSlots | Return one or slots from the 'Stan' model in 'bayesGAM'
getModelSlots-method | Return one or slots from the 'Stan' model in 'bayesGAM'
getSamples | Extract the MCMC samples from an object of type 'bayesGAMfit'
getSamples-method | Extract the MCMC samples from an object of type 'bayesGAMfit'
getStanResults | Returns the 'stanfit' object generated by 'rstan'
getStanResults-method | Returns the 'stanfit' object generated by 'rstan'
L | Lag function for autoregressive models
loo_bgam | Calls the 'loo' package to perform efficient approximate leave-one-out cross-validation on models fit with 'bayesGAM'
loo_bgam-method | Calls the 'loo' package to perform efficient approximate leave-one-out cross-validation on models fit with 'bayesGAM'
loo_compare_bgam | Calls the 'loo' package to compare models fit by 'bayesGAMfit'
loo_compare_bgam-method | Calls the 'loo' package to compare models fit by 'bayesGAMfit'
mcmc_acf | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_acf-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_acf_bar | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_acf_bar-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_areas | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_areas-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_dens | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_dens-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_hex | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_hex-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_hist | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_hist-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_hist_by_chain | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_hist_by_chain-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_intervals | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_intervals-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_neff | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_neff-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_neff_data | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_neff_data-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_neff_hist | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_neff_hist-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_pairs | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_pairs-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_plots | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_rhat | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_rhat-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_rhat_data | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_rhat_data-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_rhat_hist | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_rhat_hist-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_scatter | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_scatter-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_trace | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_trace-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_violin | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_violin-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mvcorrplot | Multivariate response correlation plot for 'bayesGAMfit' objects
mvcorrplot-method | Multivariate response correlation plot for 'bayesGAMfit' objects
normal | Constructor function for Normal priors
np | Creates design matrices for univariate and bivariate applications
plot | Additional plotting for MCMC visualization and diagnostics.
plot-method | Additional plotting for MCMC visualization and diagnostics.
posterior_predict | Posterior predictive samples from models fit by 'bayesGAM'
posterior_predict-method | Posterior predictive samples from models fit by 'bayesGAM'
ppc_boxplot | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_boxplot-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_dens | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_dens-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_dens_overlay | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_dens_overlay-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_ecdf_overlay | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_ecdf_overlay-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_freqpoly | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_freqpoly-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_hist | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_hist-method | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
ppc_plots | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
predict | Posterior predictive samples from models fit by 'bayesGAM', but with new data
predict-method | Posterior predictive samples from models fit by 'bayesGAM', but with new data
reef | Coral reef data from survey data on 6 sites
show-method | Contains results from 'rstan' as well as the design matrices and other data for the model.
showPrior | Display the priors used in 'bayesGAM'
showPrior-method | Display the priors used in 'bayesGAM'
st | Constructor function for Student-t priors
summary | Summarizing Model Fits from 'bayesGAM'
summary-method | Summarizing Model Fits from 'bayesGAM'
waic_bgam | Calls the 'loo' package to calculate the widely applicable information criterion (WAIC)
waic_bgam-method | Calls the 'loo' package to calculate the widely applicable information criterion (WAIC)