Package: tulpaRatio 1.7.3

tulpaRatio: Bayesian Hierarchical Models for Ratios, Rates, and Proportions

An opinionated framework for Bayesian hierarchical modelling of ratios, rates, and proportions. Ratios are treated as derived quantities, with all inference performed on the latent processes generating the numerator and denominator. Supports shared random effects, latent factors for unmeasured confounders, spatial structure ('CAR'/'BYM2'/'GP'), spatiotemporal interaction (Knorr-Held Type I-IV), zero-inflation variants, and full uncertainty propagation to ratio posteriors. Provides multiple inference backends including custom 'HMC'/'NUTS' (default), 'Laplace' approximation, and 'Polya-Gamma' Gibbs sampling.

Authors:Gilles Colling [aut, cre, cph]

tulpaRatio_1.7.3.tar.gz
tulpaRatio_1.7.3.zip(r-4.7-x86_64)tulpaRatio_1.7.3.zip(r-4.7-arm64)tulpaRatio_1.7.3.zip(r-4.6-x86_64)tulpaRatio_1.7.3.zip(r-4.6-arm64)tulpaRatio_1.7.3.zip(r-4.5-x86_64)
tulpaRatio_1.7.3.tgz(r-4.6-x86_64)tulpaRatio_1.7.3.tgz(r-4.6-arm64)tulpaRatio_1.7.3.tgz(r-4.5-x86_64)tulpaRatio_1.7.3.tgz(r-4.5-arm64)
tulpaRatio_1.7.3.tar.gz(r-4.7-arm64)tulpaRatio_1.7.3.tar.gz(r-4.7-x86_64)tulpaRatio_1.7.3.tar.gz(r-4.6-arm64)tulpaRatio_1.7.3.tar.gz(r-4.6-x86_64)
tulpaRatio_1.7.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
tulpaRatio/json (API)

# Install 'tulpaRatio' in R:
install.packages('tulpaRatio', repos = c('https://gcol33.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gcol33/tulparatio/issues

Pkgdown/docs site:https://gillescolling.com

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library

On CRAN:

Conda:

bayesianecologyhierarchical-modelsproportionsratioscppopenmp

4.95 score 11 scripts 91 exports 51 dependencies

Last updated from:19b38ce69c. Checks:15 OK. Indexed: yes.

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windows-release-x86_64OK563
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wasm-releaseOK183

Exports:as_drawscheck_diagnosticsdiagnostic_summarydiagnosticsdraws_intervaldraws_longdraws_widegeweke_testgpu_availablegpu_infohurdle_binomialhurdle_negbinhurdle_poissoninference_mode_infolatent_factorlatent_factorsloon_divergentoi_binomialplot_acfplot_diagnosticsplot_divergencesplot_energyplot_essplot_mapplot_map_panelplot_pairsplot_rhatposterior_predictpp_checkprior_betaprior_exponentialprior_gammaprior_half_cauchyprior_half_normalprior_normalprior_pcprior_predictpriors_defaultratioratio_contrastratiod_averageratiod_benchmarkratiod_benchmark_compareratiod_beta_binomialratiod_binomialratiod_compareratiod_gamma_gammaratiod_hurdle_binomialratiod_hurdle_negbinratiod_hurdle_poisratiod_lognormalratiod_negbin_gammaratiod_negbin_negbinratiod_oibinomialratiod_poisson_gammaratiod_priorsratiod_threadsratiod_zibinomialratiod_zinegbinratiod_zipoisratiod_zoibinomialsim_ratiodsim_ratiod_sbcspatial_bym2spatial_carspatial_gpspatial_hsgpspatial_multiscalespatial_rsrspatial_svcspatiotemporalspatiotemporal_effectssvctemporaltemporal_ar1temporal_gptemporal_iidtemporal_multiscaletemporal_rtrtemporal_rw1temporal_rw2temporal_tvctratiotvcvalidate_modewaiczi_binomialzi_negbinzi_poissonzoib

Dependencies:abindbackportsbayesplotcheckmateclicpp11distributionaldplyrfarvergenericsggdistggplot2ggridgesgluegtableisobandlabelinglatticelifecycleloomagrittrMatrixmatrixStatsnumDerivpillarpkgconfigplyrposteriorpurrrquadprogR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangS7scalesstringistringrtensorAtibbletidyrtidyselecttulpatulpaMeshutf8vctrsviridisLitewithr

Random Effects
Installation | Overview | Random Intercepts | Single Grouping Factor | Multiple (Crossed) Grouping Factors | Nested Random Effects | Deep Nesting | Random Slopes | Correlated Intercept and Slope | Uncorrelated Intercept and Slope | Multiple Slopes | Formula Expansion | Interactions | Polynomials | Parameter Naming | Shared Random Effects | Default: Shared Structure | Explicit Shared Structure | Independent Structure (Use with Caution) | Extracting Random Effects | Prior Specification | Default PC Priors | Custom Priors | Latent Factors for Unmeasured Confounders | Single Latent Factor | Two Latent Factors | Latent Factors vs Random Effects | See Also
Rendered fromrandom-effects.Rmdusingknitr::rmarkdown

Last update: 2026-10-13
Started: 2026-01-09

Spatial and Temporal Models
Installation | Overview | Spatial Models | Creating Adjacency Matrices | From Coordinates (Grid Data) | From sf Objects | ICAR Model: spatial_car() | Parameters | BYM2 Model: spatial_bym2() | Extracting Spatial Effects | Temporal Models | Random Walk: temporal_rw1(), temporal_rw2() | Cyclic Random Walk | AR(1): temporal_ar1() | Group-Specific Temporal Effects | Extracting Temporal Effects | Combining Spatial and Temporal | Spatiotemporal Interaction | Interaction Types | Type I: Unstructured Interaction | Type II: Structured Time at Each Location | Type III: Structured Space at Each Time Point | Type IV: Fully Structured (Kronecker) | Non-Separable Spatiotemporal GP | Extracting Spatiotemporal Effects | Model Selection | Prior Specification | Spatial Priors | Temporal Priors | See Also
Rendered fromspatial-temporal.Rmdusingknitr::rmarkdown

Last update: 2026-10-13
Started: 2026-01-09

Complete Workflows
Installation | Overview | Workflow 1: Fisheries CPUE | Data | Model Fitting | Diagnostics | Inference | Workflow 2: Relative Abundance | Model | Results | Workflow 3: Detection Probability | Spatial Model | Spatial Predictions | Workflow 4: Temporal Trends | Model with Temporal Structure | Extract Trend | Summary | See Also
Rendered fromworkflows.Rmdusingknitr::rmarkdown

Last update: 2026-10-12
Started: 2026-01-09

Quick Start
Installation | What tulpaRatio Does | The Three Families | Basic Example: CPUE Analysis | Extract CPUE Posteriors | Formula Syntax | Combined Formula (Recommended) | Process-Specific Predictors | Random Effects | Random Intercepts | Random Slopes | Model Checking | Quick Reference | See Also
Rendered fromgetting-started.Rmdusingknitr::rmarkdown

Last update: 2026-10-12
Started: 2026-01-07

Why Ratios Are Not Data
Installation | The Core Problem | Ratios Inherit Correlated Errors | The Offset Fallacy | The tulpaRatio Solution: Joint Modelling | Why Shared Structure Matters | The Three Families | 1. Two-Process Counts: ratiod_negbin_negbin() | 2. Trial-Based: ratiod_binomial() | 3. Count/Effort: ratiod_poisson_gamma() | Full Uncertainty Propagation | When Independence Is Appropriate | Summary | Further Reading
Rendered fromphilosophy.Rmdusingknitr::rmarkdown

Last update: 2026-10-12
Started: 2026-01-07

Zero-Inflation and Hurdle Models
Installation | Overview | Available Families | Count Data (Numerator) | Proportion Data (Binomial Numerator) | Zero-Inflated Binomial | Example: Species Detection | One-Inflated Binomial | Example: Survey Completion | Zero-and-One Inflated Binomial (ZOIB) | Example: Vegetation Cover | Hurdle Binomial | Example: Occupancy with Detection | Zero-Inflated Count Models | Choosing Between Models | Model Comparison | Posterior Predictive Checks | See Also
Rendered fromzero-inflation.Rmdusingknitr::rmarkdown

Last update: 2026-10-12
Started: 2026-01-12

Readme and manuals

Help Manual

Help pageTopics
Convert a Fitted Ratio Model to a Draws Objectas_draws.ratiod_fit
Posterior Draws of a Fitted Ratio Model as a Data Frameas.data.frame.ratiod_fit
Check MCMC Diagnostics and Report Problemscheck_diagnostics
Diagnostic Summary of a Fitted Ratio Modeldiagnostic_summary print.ratiod_diagnostic_summary
Posterior Diagnostics for a Fitted Ratio Modeldiagnostics.ratiod_fit print.ratiod_diagnostics
Point Estimates and Credible Intervals for Selected Parametersdraws_interval draws_interval.ratiod_fit
Draws for Selected Parameters in Long Formatdraws_long draws_long.ratiod_fit
Draws for Selected Parameters in Wide Formatdraws_wide draws_wide.ratiod_fit
Fitted Values of a Ratio Modelfitted.ratiod_fit print.ratiod_fitted
Geweke Convergence Testgeweke_test print.ratiod_geweke
Check Whether GPU Support Is Availablegpu_available
GPU Device Informationgpu_info print.tulpaRatio_gpu_info
GPU Support Utilitiesgpu-support
Hurdle Binomial Specificationhurdle_binomial
Hurdle Negative Binomial Specificationhurdle_negbin
Hurdle Poisson Specificationhurdle_poisson
Inference Mode Informationinference_mode_info
Latent Factor Specificationlatent_factor latent_factors.ratiod_fit print.ratiod_latent
Leave-One-Out Cross-Validationloo.ratiod_fit
Number of Divergent Transitionsn_divergent
One-Inflated Binomial Specificationoi_binomial
Plot Autocorrelation Functionsplot_acf
Plot Divergent Transitionsplot_divergences
Plot the Energy Diagnostic (E-BFMI)plot_energy
Plot the Effective Sample Size Diagnosticplot_ess
Plot Spatial Predictions as a Mapplot_map
Plot Several Maps in a Gridplot_map_panel
Plot Bivariate Parameter Posteriors (Pairs Plot)plot_pairs
Plot the Rhat Convergence Diagnosticplot_rhat
Posterior Predictive Drawsposterior_predict.ratiod_fit
Posterior Predictive Checkpp_check.ratiod_fit
Predictions from a Ratio Modelpredict.ratiod_fit print.ratiod_prediction
Summarise, Print and Plot a Fitted Ratio Modelcoef.ratiod_fit coef.summary.ratiod_fit formula.ratiod_fit nobs.ratiod_fit plot.ratiod_fit print.ratiod_fit print.ratiod_sghmc print.ratiod_sgld print.ratiod_vi print.summary.ratiod_fit print.summary.ratiod_vi summary.ratiod_fit summary.ratiod_vi vcov.ratiod_fit
Beta Priorprior_beta
Exponential Priorprior_exponential
Gamma Priorprior_gamma
Half-Cauchy Priorprior_half_cauchy
Half-Normal Priorprior_half_normal
Normal Priorprior_normal
Penalized Complexity (PC) Priorprior_pc
Prior Predictive Simulationprint.ratiod_priorpred prior_predict
Default Priors for a Model Familypriors_default
Ratio Posteriors from a Ratio Modelprint.ratiod_ratio print.ratiod_ratio_summary ratio summary.ratiod_ratio
Contrasts Between Ratio Conditionsprint.ratiod_contrast ratio_contrast
Model Averaging for Ratio Modelsfitted.ratiod_average print.ratiod_average ratiod_average weights.ratiod_average
Benchmark Sampler Performanceprint.ratiod_benchmark ratiod_benchmark
Compare Benchmarks Across Configurationsratiod_benchmark_compare
Beta-Binomial Family for Overdispersed Proportionsratiod_beta_binomial
Binomial Family for Trial-Based Ratiosratiod_binomial
Compare Ratio Modelsratiod_compare
Model Familiesprint.ratiod_family ratiod_families
Gamma-Gamma Family for Continuous Ratio Dataratiod_gamma_gamma
Hurdle Binomial Familyratiod_hurdle_binomial
Hurdle Negative Binomial Familyratiod_hurdle_negbin
Hurdle Poisson Familyratiod_hurdle_pois
Latent Factors for Unmeasured Confoundersratiod_latent
Log-Normal Family for Multiplicative Processesratiod_lognormal
Negative Binomial-Gamma Family for Overdispersed Count/Effort Ratiosratiod_negbin_gamma
Negative Binomial-Negative Binomial Familyratiod_negbin_negbin
One-Inflated Binomial Familyratiod_oibinomial
Poisson-Gamma Family for Count/Effort Ratiosratiod_poisson_gamma
Prior Specification for Ratio Modelsprint.ratiod_prior print.ratiod_priors ratiod_priors
Spatial Structure Specificationsprint.ratiod_spatial ratiod_spatial
Temporal Structure Specificationsprint.ratiod_temporal ratiod_temporal
OpenMP Thread Countratiod_threads
Posterior Predictive Checks for Ratio Modelsratiod_validate
Zero-Inflated Model Familiesprint.ratiod_family_zi ratiod_zi_families
Zero-Inflated Binomial Familyratiod_zibinomial
Zero-Inflated Negative Binomial Familyratiod_zinegbin
Zero-Inflated Poisson Familyratiod_zipois
Zero-and-One-Inflated Binomial Familyratiod_zoibinomial
Simulate Data from Ratio Modelsprint.ratiod_simdata sim_ratiod
Simulate Datasets for Simulation-Based Calibrationprint.ratiod_sbc_sims sim_ratiod_sbc
BYM2 Spatial Structurespatial_bym2
CAR Spatial Structurespatial_car
Gaussian Process Spatial Structureprint.ratiod_gp spatial_gp
Hilbert Space Gaussian Process (HSGP) Spatial Structureprint.ratiod_hsgp spatial_hsgp
Multi-Scale Gaussian Process Spatial Structureprint.ratiod_multiscale spatial_multiscale
Restricted Spatial Regression (RSR)print.ratiod_rsr spatial_rsr
Spatially Varying Coefficients (SVC)print.ratiod_svc spatial_svc
Spatiotemporal Interaction Specificationsprint.ratiod_spatiotemporal spatiotemporal
Spatially Varying Coefficients of a Fitted Modelplot.ratiod_svc_posterior print.ratiod_svc_posterior summary.ratiod_svc_posterior svc svc.ratiod_fit
Temporal Effects of a Fitted Modelplot.ratiod_temporal_posterior print.ratiod_temporal_posterior summary.ratiod_temporal_posterior temporal temporal.ratiod_fit
AR1 Temporal Structure (First-Order Autoregressive)temporal_ar1
Gaussian Process Temporal Structureprint.ratiod_temporal_gp temporal_gp
IID Temporal Structure (Independent Effects)temporal_iid
Multi-Scale Temporal Structureprint.ratiod_temporal_multiscale temporal_multiscale
Restricted Temporal Regression (RTR)print.ratiod_rtr temporal_rtr
RW1 Temporal Structure (First-Order Random Walk)temporal_rw1
RW2 Temporal Structure (Second-Order Random Walk)temporal_rw2
Temporally Varying Coefficients (TVC)print.ratiod_tvc temporal_tvc
Fit a Ratio, Rate, or Proportion Modeltratio
Temporally Varying Coefficients of a Fitted Modelplot.ratiod_tvc_posterior print.ratiod_tvc_posterior summary.ratiod_tvc_posterior tvc tvc.ratiod_fit
Validate That a Fit Used the Expected Modevalidate_mode
Widely Applicable Information Criterion (WAIC)waic.ratiod_fit
Zero-Inflated Binomial Specificationzi_binomial
Zero-Inflated Negative Binomial Specificationzi_negbin
Zero-Inflated Poisson Specificationzi_poisson
Zero-Inflation and Hurdle Model Specificationsprint.ratiod_zi zi_specification
Zero-and-One-Inflated Binomial (ZOIB) Specificationzoib