# Fit Statistical Models Using Hamiltonian Monte Carlo

## Documentation for package ‘hmclearn’ version 0.0.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

coef.hmclearn | Extract Model Coefficients
diagplots | Diagnostic plots for 'hmclearn'
diagplots.hmclearn | Diagnostic plots for 'hmclearn'
Drugs | Student Drug Usage Dataset
Endometrial | Endometrial Cancer Dataset
Gdat | Count of Fresh Gopher Tortoise Shells
glmm_bin_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
glmm_poisson_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
g_glmm_bin_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
g_glmm_poisson_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
g_linear_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
g_lmm_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
g_logistic_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
g_poisson_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
hmc | Fit a generic model using Hamiltonian Monte Carlo (HMC)
hmc.fit | Fitter function for Hamiltonian Monte Carlo (HMC)
hmclearn-glm-posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
hmclearn-plots | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
leapfrog | Leapfrog Algorithm for Hamiltonian Monte Carlo
linear_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
lmm_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
logistic_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
mcmc_acf | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_acf.hmclearn | 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.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_areas | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_areas.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_dens | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_dens.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_hex | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_hex.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_hist | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_hist.hmclearn | 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.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_intervals | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_intervals.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_neff | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_neff.hmclearn | 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.hmclearn | 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.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_pairs | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_pairs.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_rhat | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_rhat.hmclearn | 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.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_scatter | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_scatter.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_trace | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_trace.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_violin | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mcmc_violin.hmclearn | Plotting for MCMC visualization and diagnostics provided by 'bayesplot' package
mh | Fit a generic model using Metropolis-Hastings (MH)
mh.fit | Fitter function for Metropolis-Hastings (MH)
neff | Effective sample size calculation
neff.hmclearn | Effective sample size calculation
plot.hmclearn | Plot Histograms of the Posterior Distribution
poisson_posterior | Sample log posterior and gradient functions for select generalized linear models and mixed effect models
predict.hmclearn | Model Predictions for HMC or MH
psrf | Calculates Potential Scale Reduction Factor (psrf), also called the Rhat statistic, from models fit via 'mh' or 'hmc'
psrf.hmclearn | Calculates Potential Scale Reduction Factor (psrf), also called the Rhat statistic, from models fit via 'mh' or 'hmc'
qfun | Multivariate Normal Density of Theta1 | Theta2
qprop | Simulate from Multivariate Normal Density for Metropolis Algorithm
summary.hmclearn | Summarizing HMC Model Fits