Templated Unified Library for Posterior Approximation in Bayesian Hierarchical Models

A general-purpose engine for fitting Bayesian hierarchical models with spatial fields, temporal effects, spatially varying coefficients, and multiple inference backends. Scalable spatial structure includes Hilbert space approximate Gaussian processes (HSGP; Riutort-Mayol et al. 2023 ), nearest-neighbor Gaussian processes (NNGP; Datta et al. 2016 ), intrinsic conditional autoregressive models (ICAR; Besag, York, and Mollie 1991 ), the reparameterized Besag-York-Mollie model (BYM2; Riebler et al. 2016 ), and stochastic partial differential equation fields (SPDE; Lindgren, Rue, and Lindstrom 2011 ). Temporal structure covers random walks, autoregressive processes, and Gaussian processes. Inference is tiered by correctness guarantee: exact Hamiltonian Monte Carlo with the No-U-Turn sampler, Laplace and nested Laplace approximations with hyperparameter integration (Rue, Martino, and Chopin 2009 ), and variational inference. Model-specific packages plug observation likelihoods into the engine through a templated C++ callback interface.


Reference manual

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install.packages("tulpa")

0.7.5 by Gilles Colling, 2 days ago


https://github.com/gcol33/tulpa, https://gillescolling.com/tulpa/


Report a bug at https://github.com/gcol33/tulpa/issues


Browse source code at https://github.com/cran/tulpa


Authors: Gilles Colling [aut, cre, cph] (ORCID: , Frances Y. Kuo [ctb, cph] (Sobol direction numbers in src/sobol_direction_numbers.h , BSD-3-clause) , Stephen Joe [ctb, cph] (Sobol direction numbers in src/sobol_direction_numbers.h , BSD-3-clause) , Arm Limited [cph] (exp and log routines in src/fastmath.h and src/fastmath_data.cpp , MIT) , The Walnutpie Developers [cph] (WALNUTS transition in inst/include/tulpa/walnuts.h , ported from walnutpie , MIT)


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports Rcpp, Matrix, tulpaMesh, generics, stats, tools, utils, methods, graphics, grDevices

Suggests testthat, bayesplot, coda, ggplot2, sf, terra, knitr, rmarkdown, posterior, loo, rstantools, lme4, nlme, lmtest, numDeriv, spdep, MASS, betareg, glmmTMB, pscl, tweedie, fmesher, patchwork, stars, statmod, withr

Linking to Rcpp, RcppEigen, Matrix

System requirements: C++17


See at CRAN