Fit Statistical Models Using Hamiltonian Monte Carlo

Documentation for package ‘hmclearn’ version 0.0.5

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