Template Unified Latent Process Architecture for Bayesian Hierarchical Models

Documentation for package ‘tulpa’ version 0.2.0

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-- A --

adjacency	Construct a spatial adjacency graph for areal models
adjacency.data.frame	Construct a spatial adjacency graph for areal models
adjacency.default	Construct a spatial adjacency graph for areal models
adjacency.sf	Construct a spatial adjacency graph for areal models
adjacency.SpatRaster	Construct a spatial adjacency graph for areal models
adjacency.stars	Construct a spatial adjacency graph for areal models
agq_fit	Adaptive Gauss-Hermite quadrature for one-RE GLMMs
as_draws	Posterior draws in the posterior package's format
as_draws.tulpa_fit	Posterior draws in the posterior package's format
as_draws_array	Posterior draws in the posterior package's format
as_draws_array.tulpa_fit	Posterior draws in the posterior package's format
as_draws_df	Posterior draws in the posterior package's format
as_draws_df.tulpa_fit	Posterior draws in the posterior package's format
as_draws_matrix	Posterior draws in the posterior package's format
as_draws_matrix.tulpa_fit	Posterior draws in the posterior package's format
as_draws_rvars	Posterior draws in the posterior package's format
as_draws_rvars.tulpa_fit	Posterior draws in the posterior package's format
auto_grid	Mark an outer-grid setting as a default rather than a pin

-- B --

bayes_R2	Bayesian R-squared
bayes_R2.tulpa_fit	Bayesian R-squared
bridge_sampling	Bridge sampling for marginal likelihood

-- C --

check_adjacency	Validate a spatial adjacency matrix
check_diagnostics	Quick convergence check
check_model	Diagnostic panel plot
check_model.default	Diagnostic panel plot
coef.tulpa_fit	Fixed-effect coefficients
compare_models	Compare models by information criteria
confint.tulpa_fit	Credible intervals for the fixed effects
cpo	DIC and CPO
cpo.default	DIC and CPO
criteria_doors	DIC and CPO

-- D --

diagnostics	Posterior diagnostics for a fitted model
diagnostics.default	Posterior diagnostics for a fitted model
diagnostics.sbc	Posterior diagnostics for a fitted model
diagnostic_summary	Comprehensive Diagnostic Summary
dic	DIC and CPO
dic.default	DIC and CPO
durbin_watson	Durbin-Watson test for temporal autocorrelation

-- F --

fitted.tulpa_fit	Fitted values (population level)
fit_spde	Fit a Spatial Model using SPDE Laplace Approximation
fit_st_nested	Fit an additive spatiotemporal GLM by nested Laplace
fixef	Fixed-effect coefficients (lme4-compatible)
fixef.tulpa_fit	Fixed-effect coefficients (lme4-compatible)

-- G --

geweke_test	Geweke Convergence Test
glance.tulpa_fit	Model-level summary statistics (broom-compatible)

-- I --

imh_laplace	Independence Metropolis-Hastings with Laplace proposal
inference_mode_info	Print inference mode information
is_auto_grid	Is an outer-grid setting marked as a default?

-- L --

laplace_diagnostics	Approximation-reliability diagnostics for a deterministic nested-Laplace fit
latent	Mark an expression as a latent block in a tulpa formula
latent_factor	Create a latent factor specification
latent_factors	Extract latent factor posteriors from fit
logLik.tulpa_fit	Log-likelihood at the posterior mean

-- M --

mala	Metropolis-Adjusted Langevin Algorithm (MALA)
mcmc_draws	MCMC chain draws from a fit
model_average	Model-averaged predictions
moran_i	Moran's I test for spatial autocorrelation in residuals

-- N --

nobs.tulpa_fit	Number of observations in a tulpa fit
node_index	Map cell identifiers to graph node indices
n_divergent	Number of divergent transitions

-- P --

pathfinder	Pathfinder: variational warm-start via L-BFGS + ELBO scoring
pit_residuals	PIT (Probability Integral Transform) residuals
pit_residuals.default	PIT (Probability Integral Transform) residuals
plot.sbc	Simulation-based calibration
plot.tulpa_fit	Plot fixed-effect posteriors
plot.tulpa_prior_predict	Plot method for tulpa_prior_predict
plot.tulpa_st_summary	Plot method for spatiotemporal effects
plot.tulpa_svc_posterior	Plot method for tulpa_svc_posterior
plot.tulpa_temporal_posterior	Plot method for tulpa_temporal_posterior
plot.tulpa_tvc_posterior	Plot method for tulpa_tvc_posterior
plot_acf	Plot Autocorrelation Functions
plot_divergences	Plot Divergent Transitions
plot_energy	Plot Energy Diagnostic (E-BFMI)
plot_ess	Plot Effective Sample Size Diagnostic
plot_map	Plot spatial predictions as a map
plot_map_panel	Plot multiple maps in a grid
plot_pairs	Plot Bivariate Parameter Posteriors (Pairs Plot)
plot_rhat	Plot Rhat Convergence Diagnostic
posterior_predict	Posterior predictive replicates
posterior_predict.tulpa_fit	Posterior predictive replicates
posterior_sample	Posterior parameter sample from a fit
post_hoc_lm	Fit a post-hoc linear model on estimated parameters
pp_check	Posterior predictive check
pp_check.tulpa_fit	Posterior predictive check
predict.tulpa_fit	Predict at new covariate values (population level)
print.tulpa_diagnostic_summary	Print method for diagnostic summary
print.tulpa_geweke	Print method for Geweke test
print.tulpa_gp	Print method for tulpa_gp
print.tulpa_hsgp	Print method for tulpa_hsgp
print.tulpa_latent	Print method for tulpa_latent
print.tulpa_multiscale	Print method for tulpa_multiscale
print.tulpa_nested_laplace	Print method for nested-Laplace fits
print.tulpa_prior	Print method for tulpa_prior
print.tulpa_priors	Print method for tulpa_priors
print.tulpa_prior_predict	Print method for tulpa_prior_predict
print.tulpa_rsr	Print method for tulpa_rsr
print.tulpa_simulate	Print method for tulpa_simulate
print.tulpa_spatial	Print method for tulpa_spatial
print.tulpa_svc	Print method for tulpa_svc
print.tulpa_svc_posterior	Print method for tulpa_svc_posterior
print.tulpa_temporal	Print method for tulpa_temporal
print.tulpa_temporal_gp	Print method for tulpa_temporal_gp
print.tulpa_temporal_multiscale	Print method for tulpa_temporal_multiscale
print.tulpa_temporal_posterior	Print method for tulpa_temporal_posterior
print.tulpa_tvc	Print method for tulpa_tvc
print.tulpa_tvc_posterior	Print method for tulpa_tvc_posterior
priors_default	Show default priors for a tulpa family
prior_beta	Beta prior
prior_exponential	Exponential prior
prior_from_spec	Build a 'prior' list for 'tulpa_nested_laplace()' from a tulpa spec object
prior_gamma	Gamma prior
prior_half_cauchy	Half-Cauchy prior
prior_half_normal	Half-normal prior
prior_normal	Normal prior
prior_pc	Penalized complexity (PC) prior
prior_predict	Prior predictive simulation

-- R --

ranef	Random-effect summaries
ranef.tulpa_fit	Random-effect summaries
residuals.tulpa_fit	Residuals from a tulpa fit
re_cov_pc_lkj_prior	PC + LKJ hyperprior for a random-effect covariance
rubins_pool	Pool multiple imputation draws via Rubin's rules

-- S --

sbc	Simulation-based calibration
sbc.character	Simulation-based calibration
sbc.default	Simulation-based calibration
sbc_discrete	Predictive shapes an SBC fitter reports
sbc_draws	Predictive shapes an SBC fitter reports
sbc_mixture	Predictive shapes an SBC fitter reports
sbc_normal	Predictive shapes an SBC fitter reports
sbc_predictive	Predictive shapes an SBC fitter reports
sbc_rank	Predictive shapes an SBC fitter reports
select_main_params	Select the "main" model parameters for diagnostic display
simulate.tulpa_fit	Simulate responses from a fitted tulpa model
smooth_effects	Extract fitted covariate smooths
spatial	Areal spatially varying coefficient field
spatial_bym2	BYM2 spatial structure
spatial_car	CAR / ICAR spatial structure
spatial_car_proper	Proper CAR spatial structure
spatial_gp	Gaussian process spatial structure (NNGP)
spatial_multiscale	Multi-Scale Gaussian Process spatial structure
spatial_range	Extract spatial range and variance from a fitted spatial model
spatial_rsr	Restricted Spatial Regression (RSR)
spatial_spde	SPDE Spatial Field (Matern via Triangular Mesh)
spatial_spde_custom	SPDE Spatial Field from Custom Matrices
spatial_svc	Spatially varying coefficient structure
spatiotemporal	Spatiotemporal interaction specifications for tulpa
spatiotemporal_effects	Extract spatiotemporal effects from fitted model
spatiotemporal_effects.tulpa_fit	Extract spatiotemporal effects from fitted model
spatiotemporal_gp	Non-separable spatiotemporal GP
summary.sbc	Simulation-based calibration
summary.tulpa_fit	Posterior summary of the fixed effects
summary.tulpa_svc_posterior	Summary method for tulpa_svc_posterior
summary.tulpa_temporal_posterior	Summary method for tulpa_temporal_posterior
summary.tulpa_tvc_posterior	Summary method for tulpa_tvc_posterior
svc	Extract spatially-varying coefficients from a fitted model
svc.tulpa_fit	Extract spatially-varying coefficients from a fitted model

-- T --

temporal	Extract temporal effects from a fitted model
temporal.tulpa_fit	Extract temporal effects from a fitted model
temporal_ar	AR(p) temporal latent field (general-order autoregressive)
temporal_ar1	AR1 temporal structure (First-order Autoregressive)
temporal_ar2	AR(2) temporal latent field (second-order autoregressive)
temporal_corr	Extract temporal correlation parameters from a fitted model
temporal_gp	Gaussian Process temporal structure
temporal_multiscale	Multi-scale temporal structure
temporal_rtr	Restricted temporal regression (RTR)
temporal_rw1	RW1 temporal structure (First-order Random Walk)
temporal_rw2	RW2 temporal structure (Second-order Random Walk)
temporal_tvc	Time-varying coefficient structure
test_dispersion	Test for over- or underdispersion
test_dispersion.default	Test for over- or underdispersion
test_outliers	Test for outliers (simulation envelope)
test_outliers.default	Test for outliers (simulation envelope)
test_uniformity	Test uniformity of PIT residuals
test_zero_inflation	Test for zero inflation
test_zero_inflation.default	Test for zero inflation
tgmrf	User-defined GMRF latent block
tgmrf_cpp	User-defined GMRF latent block, compiled C++ backend
tidy.tulpa_fit	Tidy fixed-effect table (broom-compatible)
tulpa	Fit a tulpa model
tulpa_bar_field_replicate	Replicate an areal graph across the levels of a factor (replicated CAR)
tulpa_bar_field_specs	Expand a varying-coefficient bar into per-column field specs
tulpa_cache_clear	Remove compiled blocks from the tgmrf_cpp() cache
tulpa_cache_dir	Default cache directory for 'tgmrf_cpp()'-compiled DLLs
tulpa_check_control	Validate a 'control = list()' surface against its canonical key set
tulpa_criteria	Model criteria from a pointwise log-likelihood
tulpa_diagnostics	Simulation-Based Diagnostics for tulpa Models
tulpa_draws_array	Posterior draws as a 3D array
tulpa_eb	Empirical-Bayes random-effect covariances
tulpa_em_laplace	Fit a latent-variable model via EM + Laplace approximation
tulpa_em_mc	Generic Monte-Carlo EM driver
tulpa_ep	Expectation-Propagation fit for a GLM
tulpa_family	Construct a minimal tulpa_family for simulation
tulpa_formula	Formula parsing for tulpa models
tulpa_gaussian	Fit a Gaussian linear model via tulpa's generic engine
tulpa_gibbs	Fit via Polya-Gamma Gibbs sampler
tulpa_hyper_grid	Outer hyperparameter-grid integration with a user-supplied inner fit
tulpa_integrator	Select the symplectic integrator for HMC and NUTS
tulpa_is_spatial_bar	Recognize an inline varying-coefficient bar
tulpa_kfold	K-fold cross-validation for a tulpa fit
tulpa_laplace	Fit a model via Laplace approximation
tulpa_laplace_beta	Fit a beta-regression model via Laplace, estimating the precision
tulpa_latent	Latent Factor Specification for Unmeasured Confounders
tulpa_loglik	Streaming pointwise log-likelihood
tulpa_multinomial	Multinomial (nominal K-class) logistic regression via Laplace
tulpa_nested_laplace	Nested Laplace approximation for latent Gaussian models
tulpa_nested_laplace_joint	Joint multi-likelihood nested Laplace approximation
tulpa_nuts_beta	Fit a beta-regression model via NUTS (joint sampling of beta + log_phi)
tulpa_nuts_spde	Sample an SPDE GLM via NUTS, optionally jointly over Matern hypers
tulpa_ordinal	Ordinal (ordered K-class) cumulative-logit regression via Laplace
tulpa_parse_formula	Parse a mixed-model formula
tulpa_pit	Probability integral transform from a predictive CDF
tulpa_posterior_draws	Posterior draws from a nested-Laplace fit
tulpa_posterior_draws.tulpa_nested_laplace_joint	Posterior draws from a joint nested-Laplace fit
tulpa_powerscale_sensitivity	Power-scaling prior / likelihood sensitivity
tulpa_priors	Prior specification for tulpa models
tulpa_profile	Profile the inner Laplace solve by phase
tulpa_psis	Pareto-smoothed importance sampling
tulpa_reloo	Selective refit of high-Pareto-k observations (reloo)
tulpa_re_aghq	Adaptive Gauss-Hermite refinement of a grouped random-effect covariance
tulpa_re_cov_gibbs	Gibbs estimation of random-effect covariances (exact-target debias)
tulpa_re_cov_nested	Nested-Laplace integration over random-effect covariances
tulpa_simulate	Simulate data from a tulpa model
tulpa_spatial	Spatial structure specifications for tulpa
tulpa_temporal	Temporal structure specifications for tulpa
tulpa_tgmrf	Fit a custom tgmrf latent block
tulpa_validate	Posterior predictive checks for tulpa models
tulpa_variogram	Empirical semivariogram of residuals
tvc	Extract temporally-varying coefficients from a fitted model
tvc.tulpa_fit	Extract temporally-varying coefficients from a fitted model

-- V --

validate_mode	Validate that a fit used the expected mode
VarCorr	Random-effect variances and correlations
VarCorr.tulpa_fit	Random-effect variances and correlations
vcov.tulpa_fit	Variance-covariance matrix of the fixed effects

-- W --

with_tulpa_integrator

Run an expression under a chosen symplectic integrator