{ "_id": "6ad38309b41a16bdd47c00bb", "Package": "tulpaRatio", "URL": "https://github.com/gcol33/tulpaRatio,\nhttps://gillescolling.com/tulpaRatio/", "BugReports": "https://github.com/gcol33/tulpaRatio/issues", "Title": "Bayesian Hierarchical Models for Ratios, Rates, and Proportions", "Version": "1.7.3", "Authors@R": "person(\"Gilles\", \"Colling\", email = \"gilles.colling051@gmail.com\", role = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-3070-6066\"))", "Description": "An opinionated framework for Bayesian hierarchical\nmodelling of ratios, rates, and proportions. Ratios are treated\nas derived quantities, with all inference performed on the\nlatent processes generating the numerator and denominator.\nSupports shared random effects, latent factors for unmeasured\nconfounders, spatial structure ('CAR'/'BYM2'/'GP'),\nspatiotemporal interaction (Knorr-Held Type I-IV),\nzero-inflation variants, and full uncertainty propagation to\nratio posteriors. Provides multiple inference backends\nincluding custom 'HMC'/'NUTS' (default), 'Laplace'\napproximation, and 'Polya-Gamma' Gibbs sampling.", "Language": "en-US", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "Roxygen": "list(markdown = TRUE)", "Additional_repositories": "https://gcol33.r-universe.dev", "Config/testthat/edition": "3", "VignetteBuilder": "knitr", "Config/roxygen2/version": "8.1.0", "Config/pak/sysreqs": "cmake libicu-dev", "Repository": "https://gcol33.r-universe.dev", "Date/Publication": "2026-10-17 11:12:38 UTC", "RemoteUrl": "https://github.com/gcol33/tulparatio", "RemoteRef": "HEAD", "RemoteSha": "318fa288948b1541514177240929dc0a5a2cecd2", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-10-17 14:00:48 UTC", "User": "root" }, "Author": "Gilles Colling [aut, cre, cph] (ORCID:\n)", "Maintainer": "Gilles Colling ", "_user": "gcol33", "_type": "src", "_file": "tulpaRatio_1.7.3.tar.gz", "_fileid": "https://r2.ropensci.org/70ed7b8e97b73fa0a23d2f50ab1a2492541ac8f7825c4daff40465c14f867c28", "_filesize": 1701866, "_sha256": "70ed7b8e97b73fa0a23d2f50ab1a2492541ac8f7825c4daff40465c14f867c28", "_expires": "2027-01-25T14:15:35.000Z", "_created": "2026-10-17T14:00:48.000Z", "_published": "2026-10-17T14:15:37.467Z", "_buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890", "_status": "success", "_host": "GitHub-Actions", "_jobs": [ { "job": 117414772599, "time": 390, "config": "linux-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12103062848" }, { "job": 117414772590, "time": 421, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12103057973" }, { "job": 117414772656, "time": 366, "config": "linux-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12103273934" }, { "job": 117414772600, "time": 487, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12103502663" }, { "job": 117414772720, "time": 382, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "12103053145" }, { "job": 117414772659, "time": 722, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12103607224" }, { "job": 117414772652, "time": 429, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12103422210" }, { "job": 117414772731, "time": 570, "config": "macos-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12103018511" }, { "job": 117413230049, "time": 455, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "12102783318" }, { "job": 117414772613, "time": 232, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "12102429516" }, { "job": 117414772574, "time": 578, "config": "windows-devel-arm64", "r": "4.7.0", "check": "OK", "artifact": "12103277690" }, { "job": 117414772679, "time": 471, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "12103945284" }, { "job": 117414772750, "time": 651, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "12104095232" }, { "job": 117414772640, "time": 527, "config": "windows-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "12103472746" }, { "job": 117414772607, "time": 662, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "12103058346" } ], "_upstream": "https://github.com/gcol33/tulparatio", "_commit": { "id": "318fa288948b1541514177240929dc0a5a2cecd2", "author": "Gilles Colling ", "committer": "Gilles Colling ", "message": "fix(spatiotemporal): margin penalty normalizer moves with the GP ranges and the AR1 rho (#151, #152)\n\nThe interaction's density corrected the soft sum-to-zero penalty's\nnormalizer by a count of pinned directions times 0.5 log(tau). Where the\nprior is proper in a pinned direction, the variance there depends on other\nparameters too, and the omitted part tilted their posteriors.\n\nGP types now carry 0.5 log|I + B'SB|, formed from the NNGP factorization\nwith one (S+T)x(S+T) Cholesky and differentiated analytically in the same\npass; the dense determinant agrees to 1e-8. On the spatial-temporal\nvignette's model the omitted part rose about 18 nats with the spatial\nrange; chain 2 sat at phi_st_space 8.5 with R-hat 1.83 and 508 divergences.\nNow both chains sit near 0.15, largest R-hat 1.03, 56 divergences.\n\nType II and IV with an AR1 time margin add 0.5 (S-1) log(1'R^-1 1), plus\n0.5 log|R^-1| under Type II; the penalised prior's dense integral no longer\nmoves with rho (it fell 6.7 nats from rho 0 to 0.9 on a 5x4 grid).\n\nCo-Authored-By: Claude Opus 5.5 \nClaude-Session: https://claude.ai/code/session_011gDHZscgkTTRmo8iRPR71G\n", "time": 1792235558 }, "_maintainer": { "name": "Gilles Colling", "email": "gilles.colling051@gmail.com", "login": "gcol33", "linkedin": "in/gilles-colling-0b3747306", "orcid": "0000-0003-3070-6066", "twitter": "@Gilles__Colling", "description": "Building tools for ecology in R, C++, and Rust.\nWhy did Microsoft have to buy it. Sadge :(", "uuid": 25009600 }, "_distro": "resolute", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "Rcpp", "role": "LinkingTo" }, { "package": "RcppEigen", "role": "LinkingTo" }, { "package": "tulpa", "version": ">= 0.7.5", "role": "LinkingTo" }, { "package": "bayesplot", "role": "Imports" }, { "package": "posterior", "role": "Imports" }, { "package": "loo", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "tulpa", "version": ">= 0.7.5", "role": "Imports" }, { "package": "Rcpp", "version": ">= 1.0.0", "role": "Imports" }, { "package": "patchwork", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "gridExtra", "role": "Suggests" }, { "package": "stars", "role": "Suggests" }, { "package": "sf", "role": "Suggests" }, { "package": "Matrix", "role": "Suggests" }, { "package": "MASS", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "svglite", "role": "Suggests" } ], "_owner": "gcol33", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-02", "n": 22 }, { "week": "2026-03", "n": 42 }, { "week": "2026-04", "n": 15 }, { "week": "2026-06", "n": 2 }, { "week": "2026-07", "n": 1 }, { "week": "2026-08", "n": 1 }, { "week": "2026-09", "n": 9 }, { "week": "2026-10", "n": 10 }, { "week": "2026-11", "n": 1 }, { "week": "2026-12", "n": 4 }, { "week": "2026-18", "n": 2 }, { "week": "2026-19", "n": 7 }, { "week": "2026-20", "n": 2 }, { "week": "2026-21", "n": 11 }, { "week": "2026-22", "n": 4 }, { "week": "2026-24", "n": 2 }, { "week": "2026-25", "n": 1 }, { "week": "2026-29", "n": 4 }, { "week": "2026-30", "n": 17 }, { "week": "2026-31", "n": 11 }, { "week": "2026-32", "n": 11 }, { "week": "2026-34", "n": 13 }, { "week": "2026-35", "n": 30 }, { "week": "2026-38", "n": 1 }, { "week": "2026-40", "n": 14 }, { "week": "2026-41", "n": 9 }, { "week": "2026-42", "n": 15 } ], "_tags": [ { "name": "v0.9.0", "date": "2026-01-09" }, { "name": "v1.0.0", "date": "2026-01-09" }, { "name": "v0.9.4-benchmark", "date": "2026-01-14" }, { "name": "v1.2.2", "date": "2026-01-14" }, { "name": "v1.2.3", "date": "2026-01-14" }, { "name": "v1.2.4", "date": "2026-01-14" }, { "name": "v1.2.2-lbfgs", "date": "2026-01-18" }, { "name": "v1.2.2-phase1-complete", "date": "2026-01-18" }, { "name": "v1.2.1-binomial-zi", "date": "2026-01-19" }, { "name": "v1.3.0", "date": "2026-01-25" } ], "_topics": [ "bayesian", "ecology", "hierarchical-models", "proportions", "ratios", "cpp", "openmp" ], "_stars": 0, "_contributors": [ { "user": "gcol33", "count": 253, "uuid": 25009600 } ], "_userbio": { "uuid": 25009600, "type": "user", "name": "Gilles Colling", "followers": 10, "description": "Building tools for ecology in R, C++, and Rust.\nWhy did Microsoft have to buy it. Sadge :(" }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/tulpaRatio" }, "_devurl": "https://github.com/gcol33/tulparatio", "_pkgdown": "https://gillescolling.com/tulpaRatio/", "_searchresults": 11, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/readme.html", "extra/readme.md", "extra/tulpaRatio.html", "LICENSE" ], "_cranurl": false, "_exports": [ "as_draws", "check_diagnostics", "diagnostic_summary", "diagnostics", "draws_interval", "draws_long", "draws_wide", "geweke_test", "gpu_available", "gpu_info", "hurdle_binomial", "hurdle_negbin", "hurdle_poisson", "inference_mode_info", "latent_factor", "latent_factors", "loo", "n_divergent", "oi_binomial", "plot_acf", "plot_diagnostics", "plot_divergences", "plot_energy", "plot_ess", "plot_map", "plot_map_panel", "plot_pairs", "plot_rhat", "posterior_predict", "pp_check", "prior_beta", "prior_exponential", "prior_gamma", "prior_half_cauchy", "prior_half_normal", "prior_normal", "prior_pc", "prior_predict", "priors_default", "ratio", "ratio_contrast", "ratiod_average", "ratiod_benchmark", "ratiod_benchmark_compare", "ratiod_beta_binomial", "ratiod_binomial", "ratiod_compare", "ratiod_gamma_gamma", "ratiod_hurdle_binomial", "ratiod_hurdle_negbin", "ratiod_hurdle_pois", "ratiod_lognormal", "ratiod_negbin_gamma", "ratiod_negbin_negbin", "ratiod_oibinomial", "ratiod_poisson_gamma", "ratiod_priors", "ratiod_threads", "ratiod_zibinomial", "ratiod_zinegbin", "ratiod_zipois", "ratiod_zoibinomial", "sim_ratiod", "sim_ratiod_sbc", "spatial_bym2", "spatial_car", "spatial_gp", "spatial_hsgp", "spatial_multiscale", "spatial_rsr", "spatial_svc", "spatiotemporal", "spatiotemporal_effects", "svc", "temporal", "temporal_ar1", "temporal_gp", "temporal_iid", "temporal_multiscale", "temporal_rtr", "temporal_rw1", "temporal_rw2", "temporal_tvc", "tratio", "tvc", "validate_mode", "waic", "zi_binomial", "zi_negbin", "zi_poisson", "zoib" ], "_help": [ { "page": "as_draws", "title": "Convert a Fitted Ratio Model to a Draws Object", "topics": [ "as_draws.ratiod_fit" ] }, { "page": "as.data.frame.ratiod_fit", "title": "Posterior Draws of a Fitted Ratio Model as a Data Frame", "topics": [ "as.data.frame.ratiod_fit" ] }, { "page": "as.matrix.ratiod_priorpred", "title": "Draw matrices of predictive and simulated quantities", "topics": [ "as.matrix.ratiod_ppred", "as.matrix.ratiod_prediction_draws", "as.matrix.ratiod_priorpred", "print.ratiod_ppred", "print.ratiod_prediction_draws" ] }, { "page": "check_diagnostics", "title": "Check MCMC Diagnostics and Report Problems", "topics": [ "check_diagnostics" ] }, { "page": "diagnostic_summary", "title": "Diagnostic Summary of a Fitted Ratio Model", "topics": [ "diagnostic_summary", "print.ratiod_diagnostic_summary" ] }, { "page": "diagnostics.ratiod_fit", "title": "Posterior Diagnostics for a Fitted Ratio Model", "topics": [ "diagnostics.ratiod_fit", "print.ratiod_diagnostics" ] }, { "page": "draws_interval", "title": "Point Estimates and Credible Intervals for Selected Parameters", "topics": [ "draws_interval", "draws_interval.ratiod_fit" ] }, { "page": "draws_long", "title": "Draws for Selected Parameters in Long Format", "topics": [ "draws_long", "draws_long.ratiod_fit" ] }, { "page": "draws_wide", "title": "Draws for Selected Parameters in Wide Format", "topics": [ "draws_wide", "draws_wide.ratiod_fit" ] }, { "page": "fitted.ratiod_fit", "title": "Fitted Values of a Ratio Model", "topics": [ "fitted.ratiod_fit", "print.ratiod_fitted" ] }, { "page": "geweke_test", "title": "Geweke Convergence Test", "topics": [ "geweke_test", "print.ratiod_geweke" ] }, { "page": "gpu_available", "title": "Check Whether GPU Support Is Available", "topics": [ "gpu_available" ] }, { "page": "gpu_info", "title": "GPU Device Information", "topics": [ "gpu_info", "print.tulpaRatio_gpu_info" ] }, { "page": "gpu-support", "title": "GPU Support Utilities", "topics": [ "gpu-support" ] }, { "page": "hurdle_binomial", "title": "Hurdle Binomial Specification", "topics": [ "hurdle_binomial" ] }, { "page": "hurdle_negbin", "title": "Hurdle Negative Binomial Specification", "topics": [ "hurdle_negbin" ] }, { "page": "hurdle_poisson", "title": "Hurdle Poisson Specification", "topics": [ "hurdle_poisson" ] }, { "page": "inference_mode_info", "title": "Inference Mode Information", "topics": [ "inference_mode_info" ] }, { "page": "latent_factor", "title": "Latent Factor Specification", "topics": [ "latent_factor", "latent_factors.ratiod_fit", "print.ratiod_latent" ] }, { "page": "loo.ratiod_fit", "title": "Leave-One-Out Cross-Validation", "topics": [ "loo.ratiod_fit" ] }, { "page": "n_divergent", "title": "Number of Divergent Transitions", "topics": [ "n_divergent" ] }, { "page": "oi_binomial", "title": "One-Inflated Binomial Specification", "topics": [ "oi_binomial" ] }, { "page": "plot_acf", "title": "Plot Autocorrelation Functions", "topics": [ "plot_acf" ] }, { "page": "plot_divergences", "title": "Plot Divergent Transitions", "topics": [ "plot_divergences" ] }, { "page": "plot_energy", "title": "Plot the Energy Diagnostic (E-BFMI)", "topics": [ "plot_energy" ] }, { "page": "plot_ess", "title": "Plot the Effective Sample Size Diagnostic", "topics": [ "plot_ess" ] }, { "page": "plot_map", "title": "Plot Spatial Predictions as a Map", "topics": [ "plot_map" ] }, { "page": "plot_map_panel", "title": "Plot Several Maps in a Grid", "topics": [ "plot_map_panel" ] }, { "page": "plot_pairs", "title": "Plot Bivariate Parameter Posteriors (Pairs Plot)", "topics": [ "plot_pairs" ] }, { "page": "plot_rhat", "title": "Plot the Rhat Convergence Diagnostic", "topics": [ "plot_rhat" ] }, { "page": "posterior_predict.ratiod_fit", "title": "Posterior Predictive Draws", "topics": [ "posterior_predict.ratiod_fit" ] }, { "page": "pp_check", "title": "Posterior Predictive Check", "topics": [ "pp_check.ratiod_fit" ] }, { "page": "predict.ratiod_fit", "title": "Predictions from a Ratio Model", "topics": [ "predict.ratiod_fit", "print.ratiod_prediction" ] }, { "page": "summary.ratiod_fit", "title": "Summarise, Print and Plot a Fitted Ratio Model", "topics": [ "coef.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" ] }, { "page": "prior_beta", "title": "Beta Prior", "topics": [ "prior_beta" ] }, { "page": "prior_exponential", "title": "Exponential Prior", "topics": [ "prior_exponential" ] }, { "page": "prior_gamma", "title": "Gamma Prior", "topics": [ "prior_gamma" ] }, { "page": "prior_half_cauchy", "title": "Half-Cauchy Prior", "topics": [ "prior_half_cauchy" ] }, { "page": "prior_half_normal", "title": "Half-Normal Prior", "topics": [ "prior_half_normal" ] }, { "page": "prior_normal", "title": "Normal Prior", "topics": [ "prior_normal" ] }, { "page": "prior_pc", "title": "Penalized Complexity (PC) Prior", "topics": [ "prior_pc" ] }, { "page": "prior_predict", "title": "Prior Predictive Simulation", "topics": [ "print.ratiod_priorpred", "prior_predict" ] }, { "page": "priors_default", "title": "Default Priors for a Model Family", "topics": [ "priors_default" ] }, { "page": "ratio", "title": "Ratio Posteriors from a Ratio Model", "topics": [ "print.ratiod_ratio", "print.ratiod_ratio_summary", "ratio", "summary.ratiod_ratio" ] }, { "page": "ratio_contrast", "title": "Contrasts Between Ratio Conditions", "topics": [ "print.ratiod_contrast", "ratio_contrast" ] }, { "page": "ratiod_average", "title": "Model Averaging for Ratio Models", "topics": [ "fitted.ratiod_average", "print.ratiod_average", "ratiod_average", "weights.ratiod_average" ] }, { "page": "ratiod_benchmark", "title": "Benchmark Sampler Performance", "topics": [ "print.ratiod_benchmark", "ratiod_benchmark" ] }, { "page": "ratiod_benchmark_compare", "title": "Compare Benchmarks Across Configurations", "topics": [ "ratiod_benchmark_compare" ] }, { "page": "ratiod_beta_binomial", "title": "Beta-Binomial Family for Overdispersed Proportions", "topics": [ "ratiod_beta_binomial" ] }, { "page": "ratiod_binomial", "title": "Binomial Family for Trial-Based Ratios", "topics": [ "ratiod_binomial" ] }, { "page": "ratiod_compare", "title": "Compare Ratio Models", "topics": [ "ratiod_compare" ] }, { "page": "ratiod_families", "title": "Model Families", "topics": [ "print.ratiod_family", "ratiod_families" ] }, { "page": "ratiod_gamma_gamma", "title": "Gamma-Gamma Family for Continuous Ratio Data", "topics": [ "ratiod_gamma_gamma" ] }, { "page": "ratiod_hurdle_binomial", "title": "Hurdle Binomial Family", "topics": [ "ratiod_hurdle_binomial" ] }, { "page": "ratiod_hurdle_negbin", "title": "Hurdle Negative Binomial Family", "topics": [ "ratiod_hurdle_negbin" ] }, { "page": "ratiod_hurdle_pois", "title": "Hurdle Poisson Family", "topics": [ "ratiod_hurdle_pois" ] }, { "page": "ratiod_latent", "title": "Latent Factors for Unmeasured Confounders", "topics": [ "ratiod_latent" ] }, { "page": "ratiod_lognormal", "title": "Log-Normal Family for Multiplicative Processes", "topics": [ "ratiod_lognormal" ] }, { "page": "ratiod_negbin_gamma", "title": "Negative Binomial-Gamma Family for Overdispersed Count/Effort Ratios", "topics": [ "ratiod_negbin_gamma" ] }, { "page": "ratiod_negbin_negbin", "title": "Negative Binomial-Negative Binomial Family", "topics": [ "ratiod_negbin_negbin" ] }, { "page": "ratiod_oibinomial", "title": "One-Inflated Binomial Family", "topics": [ "ratiod_oibinomial" ] }, { "page": "ratiod_poisson_gamma", "title": "Poisson-Gamma Family for Count/Effort Ratios", "topics": [ "ratiod_poisson_gamma" ] }, { "page": "ratiod_priors", "title": "Prior Specification for Ratio Models", "topics": [ "print.ratiod_prior", "print.ratiod_priors", "ratiod_priors" ] }, { "page": "ratiod_spatial", "title": "Spatial Structure Specifications", "topics": [ "print.ratiod_spatial", "ratiod_spatial" ] }, { "page": "ratiod_temporal", "title": "Temporal Structure Specifications", "topics": [ "print.ratiod_temporal", "ratiod_temporal" ] }, { "page": "ratiod_threads", "title": "OpenMP Thread Count", "topics": [ "ratiod_threads" ] }, { "page": "ratiod_validate", "title": "Posterior Predictive Checks for Ratio Models", "topics": [ "ratiod_validate" ] }, { "page": "ratiod_zi_families", "title": "Zero-Inflated Model Families", "topics": [ "print.ratiod_family_zi", "ratiod_zi_families" ] }, { "page": "ratiod_zibinomial", "title": "Zero-Inflated Binomial Family", "topics": [ "ratiod_zibinomial" ] }, { "page": "ratiod_zinegbin", "title": "Zero-Inflated Negative Binomial Family", "topics": [ "ratiod_zinegbin" ] }, { "page": "ratiod_zipois", "title": "Zero-Inflated Poisson Family", "topics": [ "ratiod_zipois" ] }, { "page": "ratiod_zoibinomial", "title": "Zero-and-One-Inflated Binomial Family", "topics": [ "ratiod_zoibinomial" ] }, { "page": "sim_ratiod", "title": "Simulate Data from Ratio Models", "topics": [ "as.data.frame.ratiod_simdata", "coef.ratiod_simdata", "print.ratiod_simdata", "sim_ratiod" ] }, { "page": "sim_ratiod_sbc", "title": "Simulate Datasets for Simulation-Based Calibration", "topics": [ "print.ratiod_sbc_sims", "sim_ratiod_sbc" ] }, { "page": "spatial_bym2", "title": "BYM2 Spatial Structure", "topics": [ "spatial_bym2" ] }, { "page": "spatial_car", "title": "CAR Spatial Structure", "topics": [ "spatial_car" ] }, { "page": "spatial_gp", "title": "Gaussian Process Spatial Structure", "topics": [ "print.ratiod_gp", "spatial_gp" ] }, { "page": "spatial_hsgp", "title": "Hilbert Space Gaussian Process (HSGP) Spatial Structure", "topics": [ "print.ratiod_hsgp", "spatial_hsgp" ] }, { "page": "spatial_multiscale", "title": "Multi-Scale Gaussian Process Spatial Structure", "topics": [ "print.ratiod_multiscale", "spatial_multiscale" ] }, { "page": "spatial_rsr", "title": "Restricted Spatial Regression (RSR)", "topics": [ "print.ratiod_rsr", "spatial_rsr" ] }, { "page": "spatial_svc", "title": "Spatially Varying Coefficients (SVC)", "topics": [ "print.ratiod_svc", "spatial_svc" ] }, { "page": "spatiotemporal", "title": "Spatiotemporal Interaction Specifications", "topics": [ "print.ratiod_spatiotemporal", "spatiotemporal" ] }, { "page": "svc", "title": "Spatially Varying Coefficients of a Fitted Model", "topics": [ "plot.ratiod_svc_posterior", "print.ratiod_svc_posterior", "summary.ratiod_svc_posterior", "svc", "svc.ratiod_fit" ] }, { "page": "temporal", "title": "Temporal Effects of a Fitted Model", "topics": [ "plot.ratiod_temporal_posterior", "print.ratiod_temporal_posterior", "summary.ratiod_temporal_posterior", "temporal", "temporal.ratiod_fit" ] }, { "page": "temporal_ar1", "title": "AR1 Temporal Structure (First-Order Autoregressive)", "topics": [ "temporal_ar1" ] }, { "page": "temporal_gp", "title": "Gaussian Process Temporal Structure", "topics": [ "print.ratiod_temporal_gp", "temporal_gp" ] }, { "page": "temporal_iid", "title": "IID Temporal Structure (Independent Effects)", "topics": [ "temporal_iid" ] }, { "page": "temporal_multiscale", "title": "Multi-Scale Temporal Structure", "topics": [ "print.ratiod_temporal_multiscale", "temporal_multiscale" ] }, { "page": "temporal_rtr", "title": "Restricted Temporal Regression (RTR)", "topics": [ "print.ratiod_rtr", "temporal_rtr" ] }, { "page": "temporal_rw1", "title": "RW1 Temporal Structure (First-Order Random Walk)", "topics": [ "temporal_rw1" ] }, { "page": "temporal_rw2", "title": "RW2 Temporal Structure (Second-Order Random Walk)", "topics": [ "temporal_rw2" ] }, { "page": "temporal_tvc", "title": "Temporally Varying Coefficients (TVC)", "topics": [ "print.ratiod_tvc", "temporal_tvc" ] }, { "page": "tratio", "title": "Fit a Ratio, Rate, or Proportion Model", "topics": [ "tratio" ] }, { "page": "tvc", "title": "Temporally Varying Coefficients of a Fitted Model", "topics": [ "plot.ratiod_tvc_posterior", "print.ratiod_tvc_posterior", "summary.ratiod_tvc_posterior", "tvc", "tvc.ratiod_fit" ] }, { "page": "validate_mode", "title": "Validate That a Fit Used the Expected Mode", "topics": [ "validate_mode" ] }, { "page": "waic.ratiod_fit", "title": "Widely Applicable Information Criterion (WAIC)", "topics": [ "waic.ratiod_fit" ] }, { "page": "zi_binomial", "title": "Zero-Inflated Binomial Specification", "topics": [ "zi_binomial" ] }, { "page": "zi_negbin", "title": "Zero-Inflated Negative Binomial Specification", "topics": [ "zi_negbin" ] }, { "page": "zi_poisson", "title": "Zero-Inflated Poisson Specification", "topics": [ "zi_poisson" ] }, { "page": "zi_specification", "title": "Zero-Inflation and Hurdle Model Specifications", "topics": [ "print.ratiod_zi", "zi_specification" ] }, { "page": "zoib", "title": "Zero-and-One-Inflated Binomial (ZOIB) Specification", "topics": [ "zoib" ] } ], "_readme": "https://github.com/gcol33/tulparatio/raw/HEAD/README.md", "_rundeps": [ "abind", "backports", "bayesplot", "checkmate", "cli", "cpp11", "distributional", "dplyr", "farver", "generics", "ggdist", "ggplot2", "ggridges", "glue", "gtable", "isoband", "labeling", "lattice", "lifecycle", "loo", "magrittr", "Matrix", "matrixStats", "numDeriv", "pillar", "pkgconfig", "plyr", "posterior", "purrr", "quadprog", "R6", "RColorBrewer", "Rcpp", "RcppEigen", "RcppParallel", "reshape2", "rlang", "S7", "scales", "stringi", "stringr", "tensorA", "tibble", "tidyr", "tidyselect", "tulpa", "tulpaMesh", "utf8", "vctrs", "viridisLite", "withr" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" }, { "shlib": "libgomp", "package": "libgomp1", "source": "gcc", "version": "16-20260322-1ubuntu1", "name": "openmp", "homepage": "http://gcc.gnu.org/", "description": "GCC OpenMP (GOMP) support library" } ], "_vignettes": [ { "source": "workflows.Rmd", "filename": "workflows.html", "title": "Complete Workflows", "author": "Gilles Colling", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2026-01-09 12:33:22", "modified": "2026-10-12 14:54:57", "commits": 5 }, { "source": "getting-started.Rmd", "filename": "getting-started.html", "title": "Quick Start", "author": "Gilles Colling", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2026-01-07 19:24:23", "modified": "2026-10-12 14:54:57", "commits": 10 }, { "source": "random-effects.Rmd", "filename": "random-effects.html", "title": "Random Effects", "author": "Gilles Colling", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2026-01-09 12:33:22", "modified": "2026-10-13 02:31:22", "commits": 9 }, { "source": "spatial-temporal.Rmd", "filename": "spatial-temporal.html", "title": "Spatial and Temporal Models", "author": "Gilles Colling", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2026-01-09 12:33:22", "modified": "2026-10-17 11:12:38", "commits": 10 }, { "source": "philosophy.Rmd", "filename": "philosophy.html", "title": "Why Ratios Are Not Data", "author": "Gilles Colling", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2026-01-07 19:24:23", "modified": "2026-10-12 14:54:57", "commits": 9 }, { "source": "zero-inflation.Rmd", "filename": "zero-inflation.html", "title": "Zero-Inflation and Hurdle Models", "author": "Gilles Colling", "engine": "knitr::rmarkdown", "headings": [ "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" ], "created": "2026-01-12 22:52:29", "modified": "2026-10-12 14:54:57", "commits": 7 } ], "_score": 4.949877704036875, "_indexed": true, "_nocasepkg": "tulparatio", "_universes": [ "gcol33" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.7.3", "date": "2026-10-17T14:04:47.000Z", "distro": "resolute", "arch": "aarch64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/e138013efd443006d959b848bbec2d4abca359b3c9d0ec94f2eefc21f93bb32d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.7.0", "os": "linux", "version": "1.7.3", "date": "2026-10-17T14:05:05.000Z", "distro": "resolute", "arch": "x86_64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/69480b5c5de5c7f860751e343fc2c3cef4aec2acfd3d8a1ed65baba0315767fd", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.6.1", "os": "linux", "version": "1.7.3", "date": "2026-10-17T14:04:38.000Z", "distro": "resolute", "arch": "aarch64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/88f32d1a9773913e1c1f5be87b75b96027f79445029b5072b92fecaad901b61e", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.6.1", "os": "linux", "version": "1.7.3", "date": "2026-10-17T14:05:09.000Z", "distro": "resolute", "arch": "x86_64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/4a286021279c05cce01a31c6658978f7116d0624793523529c2ed967d18dbfd9", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.5.3", "os": "mac", "version": "1.7.3", "date": "2026-10-17T14:06:02.000Z", "arch": "aarch64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/6910c05c6cf6c43d376db1da6b5dbcef3e567a63dcc7c7aa3314fc0e9c08b120", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.5.3", "os": "mac", "version": "1.7.3", "date": "2026-10-17T14:06:03.000Z", "arch": "x86_64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/55771bfdb24169a34c25fc4040757cda6945e05ec1b4d38fba3005541dbb3235", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.6.1", "os": "mac", "version": "1.7.3", "date": "2026-10-17T14:07:14.000Z", "arch": "aarch64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/b450945bdcb3d3f1821d6a7bb6de24cee54702102344c5da8aea4ed514e5cab2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.6.1", "os": "mac", "version": "1.7.3", "date": "2026-10-17T14:07:21.000Z", "arch": "x86_64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/635c0d55b40a7b1b6190d685631a71ff22020787f6f5c293c03fd2411bfb0348", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.6.0", "os": "wasm", "version": "1.7.3", "date": "2026-10-17T14:05:00.000Z", "arch": "emscripten", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/8151dfa79828dd14b907284a5fcec3c7b7668b7b3da7ba9715bac467c0e5f215", "status": "success", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.7.0", "os": "win", "version": "1.7.3", "date": "2026-10-17T14:06:35.000Z", "arch": "aarch64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/187d4ca1ba47885077a972088d08b7a7418eb07e8f84b414865c3bc0c29af515", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.7.0", "os": "win", "version": "1.7.3", "date": "2026-10-17T14:04:22.000Z", "arch": "x86_64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/2ea6b26e5ce61cca93cbd6a2032ffbcbe3a3af92eddda542dbf9326f44ef9e71", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.5.3", "os": "win", "version": "1.7.3", "date": "2026-10-17T14:04:06.000Z", "arch": "x86_64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/8a03a2eff0ef171f0219b0d5671fa808f230ee9ca608de4882a8091c1939831f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.6.1", "os": "win", "version": "1.7.3", "date": "2026-10-17T14:05:51.000Z", "arch": "aarch64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/ac41cdefd4d210d0d80e4b26c872a2c0efe13aef691f590ab77d2efe33984746", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" }, { "r": "4.6.1", "os": "win", "version": "1.7.3", "date": "2026-10-17T14:04:10.000Z", "arch": "x86_64", "commit": "318fa288948b1541514177240929dc0a5a2cecd2", "fileid": "https://r2.ropensci.org/526cfea6a13c79cccbae5ea70a72d94444296746850ba7be70c8ca2e0e996e3a", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gcol33/actions/runs/39038543890" } ] }