Package index • tulpaRatio

Model Fitting

Main function for fitting ratio models

tratio(): Fit a Ratio, Rate, or Proportion Model
ratiod_average() print(<ratiod_average>) fitted(<ratiod_average>) weights(<ratiod_average>): Model Averaging for Ratio Models
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(): Hurdle Negative Binomial Specification
hurdle_poisson(): Hurdle Poisson Specification
hurdle_binomial(): Hurdle Binomial Specification
zi_negbin(): Zero-Inflated Negative Binomial Specification
zi_poisson(): Zero-Inflated Poisson Specification
zi_binomial(): Zero-Inflated Binomial Specification
oi_binomial(): One-Inflated Binomial Specification
zoib(): Zero-and-One-Inflated Binomial (ZOIB) Specification
print(<ratiod_zi>): Zero-Inflation and Hurdle Model Specifications

Ratio Inference

Extract and compare ratio posteriors

ratio() summary(<ratiod_ratio>) print(<ratiod_ratio>) print(<ratiod_ratio_summary>): Ratio Posteriors from a Ratio Model
ratio_contrast() print(<ratiod_contrast>): Contrasts Between Ratio Conditions

Spatial Structure

Spatial random effect specifications

spatial_car(): CAR Spatial Structure
spatial_bym2(): BYM2 Spatial Structure
spatial_gp() print(<ratiod_gp>): Gaussian Process Spatial Structure
spatial_hsgp() print(<ratiod_hsgp>): Hilbert Space Gaussian Process (HSGP) Spatial Structure
spatial_rsr() print(<ratiod_rsr>): Restricted Spatial Regression (RSR)
spatial_svc() print(<ratiod_svc>): Spatially Varying Coefficients (SVC)
spatial_multiscale() print(<ratiod_multiscale>): Multi-Scale Gaussian Process Spatial Structure
svc() summary(<ratiod_svc_posterior>) print(<ratiod_svc_posterior>) plot(<ratiod_svc_posterior>): Spatially Varying Coefficients of a Fitted Model

Spatiotemporal Structure

Joint spatiotemporal specifications

spatiotemporal() print(<ratiod_spatiotemporal>): Spatiotemporal Interaction Specifications
reexports as_draws pp_check posterior_predict latent_factors spatiotemporal_effects loo waic diagnostics: Objects exported from other packages

Latent Factors

Latent factor specifications

latent_factor() print(<ratiod_latent>) latent_factors(<ratiod_fit>): Latent Factor Specification
reexports as_draws pp_check posterior_predict latent_factors spatiotemporal_effects loo waic diagnostics: Objects exported from other packages
ratiod_latent: Latent Factors for Unmeasured Confounders

Inference Modes

Inference tier system (Exact / Structured / Optimized)

inference_mode_info(): 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 Whether GPU Support Is Available
gpu_info() print(<tulpaRatio_gpu_info>): 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_iid(): IID Temporal Structure (Independent Effects)
temporal_gp() print(<ratiod_temporal_gp>): Gaussian Process Temporal Structure
temporal_rtr() print(<ratiod_rtr>): Restricted Temporal Regression (RTR)
temporal_tvc() print(<ratiod_tvc>): Temporally Varying Coefficients (TVC)
temporal_multiscale() print(<ratiod_temporal_multiscale>): Multi-Scale Temporal Structure
temporal() print(<ratiod_temporal_posterior>) summary(<ratiod_temporal_posterior>) plot(<ratiod_temporal_posterior>): Temporal Effects of a Fitted Model
tvc() print(<ratiod_tvc_posterior>) summary(<ratiod_tvc_posterior>) plot(<ratiod_tvc_posterior>): Temporally Varying Coefficients of a Fitted Model

Priors

Prior specification helpers

ratiod_priors() print(<ratiod_priors>) print(<ratiod_prior>): Prior Specification for Ratio Models
priors_default(): Default Priors for a Model 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() print(<ratiod_priorpred>): Prior Predictive Simulation

Model Checking

Posterior predictive checks and model comparison

pp_check(<ratiod_fit>): Posterior Predictive Check
posterior_predict(<ratiod_fit>): Posterior Predictive Draws
loo(<ratiod_fit>): Leave-One-Out Cross-Validation
waic(<ratiod_fit>): Widely Applicable Information Criterion (WAIC)
check_diagnostics(): Check MCMC Diagnostics and Report Problems
diagnostic_summary() print(<ratiod_diagnostic_summary>): Diagnostic Summary of a Fitted Ratio Model
diagnostics(<ratiod_fit>) print(<ratiod_diagnostics>): Posterior Diagnostics for a Fitted Ratio Model
geweke_test() print(<ratiod_geweke>): Geweke Convergence Test
n_divergent(): Number of Divergent Transitions

Plotting

Visualization functions

plot_acf(): Plot Autocorrelation Functions
plot_divergences(): Plot Divergent Transitions
plot_energy(): Plot the Energy Diagnostic (E-BFMI)
plot_ess(): Plot the Effective Sample Size Diagnostic
plot_map(): Plot Spatial Predictions as a Map
plot_map_panel(): Plot Several Maps in a Grid
plot_pairs(): Plot Bivariate Parameter Posteriors (Pairs Plot)
plot_rhat(): Plot the Rhat Convergence Diagnostic
print(<ratiod_sghmc>) print(<ratiod_sgld>) print(<ratiod_vi>) summary(<ratiod_vi>) print(<summary.ratiod_vi>) print(<ratiod_fit>) summary(<ratiod_fit>) print(<summary.ratiod_fit>) coef(<summary.ratiod_fit>) coef(<ratiod_fit>) vcov(<ratiod_fit>) nobs(<ratiod_fit>) formula(<ratiod_fit>) plot(<ratiod_fit>): Summarise, Print and Plot a Fitted Ratio Model
svc() summary(<ratiod_svc_posterior>) print(<ratiod_svc_posterior>) plot(<ratiod_svc_posterior>): Spatially Varying Coefficients of a Fitted Model
temporal() print(<ratiod_temporal_posterior>) summary(<ratiod_temporal_posterior>) plot(<ratiod_temporal_posterior>): Temporal Effects of a Fitted Model
tvc() print(<ratiod_tvc_posterior>) summary(<ratiod_tvc_posterior>) plot(<ratiod_tvc_posterior>): Temporally Varying Coefficients of a Fitted Model

Posterior Draws

Extract and manipulate posterior samples

as_draws(<ratiod_fit>): Convert a Fitted Ratio Model to a Draws Object
draws_long(): Draws for Selected Parameters in Long Format
draws_wide(): Draws for Selected Parameters in Wide Format
draws_interval(): Point Estimates and Credible Intervals for Selected Parameters

Simulation

Data simulation for testing

sim_ratiod() print(<ratiod_simdata>): Simulate Data from Ratio Models
sim_ratiod_sbc() print(<ratiod_sbc_sims>): Simulate Datasets for Simulation-Based Calibration

Benchmarking

Performance comparison

ratiod_benchmark() print(<ratiod_benchmark>): Benchmark Sampler Performance
ratiod_benchmark_compare(): Compare Benchmarks Across Configurations
ratiod_threads(): OpenMP Thread Count

Methods

S3 methods for ratiod objects

ratio() summary(<ratiod_ratio>) print(<ratiod_ratio>) print(<ratiod_ratio_summary>): Ratio Posteriors from a Ratio Model
print(<ratiod_sghmc>) print(<ratiod_sgld>) print(<ratiod_vi>) summary(<ratiod_vi>) print(<summary.ratiod_vi>) print(<ratiod_fit>) summary(<ratiod_fit>) print(<summary.ratiod_fit>) coef(<summary.ratiod_fit>) coef(<ratiod_fit>) vcov(<ratiod_fit>) nobs(<ratiod_fit>) formula(<ratiod_fit>) plot(<ratiod_fit>): Summarise, Print and Plot a Fitted Ratio Model
svc() summary(<ratiod_svc_posterior>) print(<ratiod_svc_posterior>) plot(<ratiod_svc_posterior>): Spatially Varying Coefficients of a Fitted Model
temporal() print(<ratiod_temporal_posterior>) summary(<ratiod_temporal_posterior>) plot(<ratiod_temporal_posterior>): Temporal Effects of a Fitted Model
tvc() print(<ratiod_tvc_posterior>) summary(<ratiod_tvc_posterior>) plot(<ratiod_tvc_posterior>): Temporally Varying Coefficients of a Fitted Model
fitted(<ratiod_fit>) print(<ratiod_fitted>): Fitted Values of a Ratio Model
ratiod_average() print(<ratiod_average>) fitted(<ratiod_average>) weights(<ratiod_average>): Model Averaging for Ratio Models
predict(<ratiod_fit>) print(<ratiod_prediction>): Predictions from a Ratio Model
as.data.frame(<ratiod_fit>): Posterior Draws of a Fitted Ratio Model as a Data Frame

Documentation

Package documentation pages

print(<ratiod_family>): Model Families
print(<ratiod_spatial>): Spatial Structure Specifications
print(<ratiod_temporal>): Temporal Structure Specifications
ratiod_validate: Posterior Predictive Checks for Ratio Models
print(<ratiod_family_zi>): Zero-Inflated Model Families