Package index • tulpaRatio

Model Fitting

Main function for fitting ratio models

tratio(): Fit a ratio, rate, or proportion model
ratiod_average(): Model averaging for tulpaRatio fits
ratiod_compare(): Compare ratio models

Model Families

Distribution families for numerator/denominator processes

ratiod_negbin_negbin(): Negative binomial - Negative binomial family
ratiod_binomial(): Binomial family for trial-based ratios
ratiod_poisson_gamma(): Poisson-Gamma family for count/effort ratios
ratiod_negbin_gamma(): Negative binomial - Gamma family for overdispersed count/effort ratios
ratiod_beta_binomial(): Beta-binomial family for overdispersed proportions
ratiod_gamma_gamma(): Gamma-Gamma family for continuous ratio data
ratiod_lognormal(): Log-normal family for multiplicative processes
ratiod_hurdle_negbin(): Hurdle negative binomial family
ratiod_hurdle_pois(): Hurdle Poisson family
ratiod_hurdle_binomial(): Hurdle binomial family
ratiod_zinegbin(): Zero-inflated negative binomial family
ratiod_zipois(): Zero-inflated Poisson family
ratiod_zibinomial(): Zero-inflated binomial family
ratiod_oibinomial(): One-inflated binomial family
ratiod_zoibinomial(): Zero-and-one inflated binomial family
hurdle_negbin(): Create a hurdle negative binomial specification
hurdle_poisson(): Create a hurdle Poisson specification
hurdle_binomial(): Create a hurdle binomial specification
zi_negbin(): Create a zero-inflated negative binomial specification
zi_poisson(): Create a zero-inflated Poisson specification
zi_binomial(): Create a zero-inflated binomial specification
oi_binomial(): Create a one-inflated binomial specification
zoib(): Create a zero-and-one-inflated binomial (ZOIB) specification
zi_specification: Zero-Inflation and Hurdle Model Specifications

Ratio Inference

Extract and compare ratio posteriors

ratio(): Extract ratio posteriors from a ratio model
ratio_contrast(): Compute contrasts between ratio conditions

Spatial Structure

Spatial random effect specifications

spatial_car(): CAR spatial structure
spatial_bym2(): BYM2 spatial structure
spatial_gp(): Gaussian Process spatial structure
spatial_hsgp(): Hilbert Space Gaussian Process (HSGP) spatial structure
spatial_rsr(): Restricted Spatial Regression (RSR)
spatial_svc(): Spatially-Varying Coefficients (SVC)
spatial_multiscale(): Multi-Scale Gaussian Process spatial structure
svc(): Extract spatially-varying coefficients from a fitted model

Spatiotemporal Structure

Joint spatiotemporal specifications

spatiotemporal(): Spatiotemporal interaction specifications for tulpaRatio
spatiotemporal_gp(): Non-separable spatiotemporal GP
spatiotemporal_effects(): Extract spatiotemporal effects from fitted model

Latent Factors

Latent factor specifications

latent_factor(): Create a latent factor specification
latent_factors(): Extract latent factor posteriors from fit
ratiod_latent: Latent Factor Specification for Unmeasured Confounders

Inference Modes

Inference tier system (Exact / Structured / Optimized)

inference_mode_info(): Print inference mode information
validate_mode(): Validate that a fit used the expected mode

GPU Support

GPU device discovery and configuration

gpu-support: GPU Support Utilities
gpu_available(): Check if GPU support is available
gpu_info(): Get GPU device information

Temporal Structure

Temporal random effect specifications

temporal_rw1(): RW1 temporal structure (First-order Random Walk)
temporal_rw2(): RW2 temporal structure (Second-order Random Walk)
temporal_ar1(): AR1 temporal structure (First-order Autoregressive)
temporal_gp(): Gaussian Process temporal structure
temporal_rtr(): Restricted Temporal Regression (RTR)
temporal_tvc(): Temporally-Varying Coefficients (TVC)
temporal_multiscale(): Multi-Scale temporal structure
temporal(): Extract temporal effects from a fitted model
tvc(): Extract temporally-varying coefficients from a fitted model

Priors

Prior specification helpers

ratiod_priors(): Prior specification for ratio models
ratiod_priors_legacy(): Legacy prior specification (deprecated)
priors_default(): Show default priors for a tulpaRatio family
prior_normal(): Normal prior
prior_half_normal(): Half-normal prior
prior_half_cauchy(): Half-Cauchy prior
prior_exponential(): Exponential prior
prior_gamma(): Gamma prior
prior_beta(): Beta prior
prior_pc(): Penalized complexity (PC) prior
prior_predict(): Prior predictive simulation

Model Checking

Posterior predictive checks and model comparison

pp_check(): Posterior predictive check
loo(<ratiod_fit>): LOO cross-validation
waic(<ratiod_fit>): WAIC computation
check_diagnostics(): Check MCMC diagnostics and print warnings
diagnostic_summary(): Comprehensive Diagnostic Summary
mcmc_diagnostics() deprecated: Compute MCMC diagnostics (Rhat, ESS) for ratiod_fit
diagnostics(<ratiod_fit>): Posterior diagnostics for a ratiod_fit
geweke_test(): Geweke Convergence Test
n_divergent(): Get number of divergent transitions

Plotting

Visualization functions

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
plot(<ratiod_fit>): Plot method for ratiod_fit
plot(<ratiod_st_summary>): Plot method for spatiotemporal effects
plot(<ratiod_svc_posterior>): Plot method for ratiod_svc_posterior
plot(<ratiod_temporal_posterior>): Plot method for ratiod_temporal_posterior
plot(<ratiod_tvc_posterior>): Plot method for ratiod_tvc_posterior

Posterior Draws

Extract and manipulate posterior samples

as_draws(): Convert ratiod_fit to posterior draws format
gather_draws(): Gather draws into long format (tidybayes-style)
spread_draws(): Spread draws into wide format (tidybayes-style)
point_interval(): Point estimates and intervals (tidybayes-style)

Simulation

Data simulation for testing

sim_ratiod(): Simulate data from ratio models
sim_ratiod_sbc(): Simulate multiple datasets for SBC

Benchmarking

Performance comparison

ratiod_benchmark(): Benchmark tulpaRatio performance
ratiod_benchmark_compare(): Compare benchmark across configurations
ratiod_threads(): Get OpenMP thread count

Methods

S3 methods for ratiod objects

print(<ratiod_average>): Print method for ratiod_average
print(<ratiod_benchmark>): Print benchmark results
print(<ratiod_contrast>): Print method for ratiod_contrast
print(<ratiod_diagnostic_summary>): Print method for diagnostic summary
print(<ratiod_diagnostics>): Print method for ratiod_diagnostics
print(<ratiod_ess>): Print method for ratiod_ess objects
print(<ratiod_family>): Print method for ratiod_family
print(<ratiod_family_zi>): Print method for zero-inflated ratiod_family
print(<ratiod_fit>): Print method for ratiod_fit
print(<ratiod_fitted>): Print method for ratiod_fitted
print(<ratiod_geweke>): Print method for Geweke test
print(<ratiod_gp>): Print method for ratiod_gp
print(<ratiod_hsgp>): Print method for ratiod_hsgp
print(<ratiod_latent>): Print method for ratiod_latent
print(<ratiod_multiscale>): Print method for ratiod_multiscale
print(<ratiod_prediction>): Print method for ratiod_prediction
print(<ratiod_prior>): Print method for ratiod_prior
print(<ratiod_priors>): Print method for ratiod_priors
print(<ratiod_ratio>): Print method for ratiod_ratio
print(<ratiod_ratio_summary>): Print method for ratiod_ratio_summary
print(<ratiod_rsr>): Print method for ratiod_rsr
print(<ratiod_rtr>): Print method for ratiod_rtr (temporal)
print(<ratiod_sbc_sims>): Print method for ratiod_sbc_sims
print(<ratiod_sghmc>): Print method for ratiod_sghmc objects
print(<ratiod_sgld>): Print method for ratiod_sgld objects
print(<ratiod_simdata>): Print method for ratiod_simdata
print(<ratiod_spatial>): Print method for ratiod_spatial
print(<ratiod_spatiotemporal>): Print method for ratiod_spatiotemporal
print(<ratiod_st_gp>): Print method for ratiod_st_gp
print(<ratiod_svc>): Print method for ratiod_svc
print(<ratiod_svc_posterior>): Print method for ratiod_svc_posterior
print(<ratiod_temporal>): Print method for ratiod_temporal
print(<ratiod_temporal_gp>): Print method for ratiod_temporal_gp
print(<ratiod_temporal_multiscale>): Print method for ratiod_temporal_multiscale
print(<ratiod_temporal_posterior>): Print method for ratiod_temporal_posterior
print(<ratiod_tvc>): Print method for ratiod_tvc
print(<ratiod_tvc_posterior>): Print method for ratiod_tvc_posterior
print(<ratiod_vi>): Print method for ratiod_vi objects
print(<ratiod_zi>): Print method for ratiod_zi objects
print(<summary.ratiod_ess>): Print method for summary.ratiod_ess
print(<summary.ratiod_vi>): Print method for summary.ratiod_vi
print(<tulpaRatio_gpu_info>): Print GPU information
summary(<ratiod_ess>): Summary method for ratiod_ess objects
summary(<ratiod_fit>): Summary method for ratiod_fit
summary(<ratiod_ratio>): Summary method for ratiod_ratio
summary(<ratiod_svc_posterior>): Summary method for ratiod_svc_posterior
summary(<ratiod_temporal_posterior>): Summary method for ratiod_temporal_posterior
summary(<ratiod_tvc_posterior>): Summary method for ratiod_tvc_posterior
summary(<ratiod_vi>): Summary method for ratiod_vi objects
fitted(<ratiod_average>): Extract predictions from ratiod_average
fitted(<ratiod_fit>): Extract fitted values from a ratio model
predict(<ratiod_fit>): Predict method for ratio models
weights(<ratiod_average>): Extract model weights from ratiod_average
as.data.frame(<ratiod_fit>): Extract posterior draws from ratiod_fit

Documentation

Package documentation pages

ratiod_families: Model families for tulpaRatio
ratiod_spatial: Spatial structure specifications for tulpaRatio
ratiod_temporal: Temporal structure specifications for tulpaRatio
ratiod_validate: Posterior predictive checks for ratio models
ratiod_zi_families: Zero-inflated model families for tulpaRatio