Generalized additive models (GAMs, Hastie & Tibshirani, 1990; Wood, 2017) are an extension of the generalized linear model that allows the effects of covariates to be modelled as smooth functions. GAMs are increasingly used in many areas of science (e.g. Pedersen, Miller, Simpson, & Ross, 2019; Simpson, 2018) because the smooth functions allow nonlinear relationships between covariates and the response to be learned from the data through the use of penalized splines. Within the R (R Core Team, 2024) ecosystem, Simon Wood's mgcv package (Wood, 2017) is widely used to fit GAMs and is a Recommended package that ships with R as part of the default install. A growing number of other R packages build upon mgcv, for example as an engine to fit specialised models not handled by mgcv itself (e.g. GJMR, Marra & Radice, 2023), or to make use of the wide range of splines available in mgcv (e.g. brms, Bürkner, 2017).
The gratia package builds upon mgcv by providing functions that make working with GAMs easier. gratia takes a tidy approach (Wickham, 2014) providing ggplot2 (Wickham, 2016) replacements for mgcv's base graphics-based plots, functions for model diagnostics and exploration of fitted models, and a family of functions for drawing samples from the posterior distribution of a fitted GAM. Additional functionality is provided to facilitate the teaching and understanding of GAMs.
This article introduces the R package evgam. The package provides functions for fitting extreme value distributions. These include the generalized extreme value and generalized Pareto distributions. The former can also be fitted through a point process representation. evgam supports quantile regression via the asymmetric Laplace distribution, which can be useful for estimating high thresholds, sometimes used to discriminate between extreme and non-extreme values. The main addition of evgam is to let extreme value distribution parameters have generalized additive model forms, which can be objec…
BHAM is a freely avaible R pakcage that implments Bayesian hierarchical additive models for high-dimensional clinical and genomic data. The package includes functions that generalized additive model, and Cox additive model with the spike-and-slab LASSO prior. These functions implement scalable and stable algorithms to estimate parameters. BHAM also provides utility functions to construct additive models in high dimensional settings, select optimal models, summarize bi-level variable selection results, and visualize nonlinear effects. The package can facilitate flexible modeling of large-scale …
neuralGAM: An R Package for Fitting Generalized Additive Neural Networks
Galician Research and Development Center in Advanced Telecommunications (Gradiant)（加利西亚先进电信研究与发展中心（Gradiant））；Galician Centre for Mathematical Research and Technology (CITMAga)（加利西亚数学研究与技术中心（CITMAga））；Universidade de Vigo, Department of Statistics and O.R. & SiDOR Group（维戈大学统计与运筹学系及SiDOR小组）
The R package abn is designed to fit additive Bayesian models to observational datasets. It contains routines to score Bayesian networks based on Bayesian or information theoretic formulations of generalized linear models. It is equipped with exact search and greedy search algorithms to select the best network. It supports a possible blend of continuous, discrete and count data and input of prior knowledge at a structural level. The Bayesian implementation supports random effects to control for one-layer clustering. In this paper, we give an overview of the methodology and illustrate the packa…
The cgam package contains routines to fit the generalized additive model where the components may be modeled with shape and smoothness assumptions. The main routine is cgam and nineteen symbolic routines are provided to indicate the relationship between the response and each predictor, which satisfies constraints such as monotonicity, convexity, their combinations, tree, and umbrella orderings. The user may specify constrained splines to fit the components for continuous predictors, and various types of orderings for the ordinal predictors. In addition, the user may specify parametrically mode…
This paper presents a high-level description of the R software package mixdistreg to fit mixture of experts distributional regression models. The proposed framework is implemented in R using the deepregression software template, which is based on TensorFlow and follows the neural structured additive learning principle. The software comprises various approaches as special cases, including mixture density networks and mixture regression approaches. Various code examples are given to demonstrate the package's functionality.
This is an overview of the R package iprior, which implements a unified methodology for fitting parametric and nonparametric regression models, including additive models, multilevel models, and models with one or more functional covariates. Based on the principle of maximum entropy, an I-prior is an objective Gaussian process prior for the regression function with covariance kernel equal to its Fisher information. The regression function is estimated by its posterior mean under the I-prior, and hyperparameters are estimated via maximum marginal likelihood. Estimation of I-prior models is simpl…
We propose an extensive framework for additive regression models for correlated functional responses, allowing for multiple partially nested or crossed functional random effects with flexible correlation structures for, e.g., spatial, temporal, or longitudinal functional data. Additionally, our framework includes linear and nonlinear effects of functional and scalar covariates that may vary smoothly over the index of the functional response. It accommodates densely or sparsely observed functional responses and predictors which may be observed with additional error and includes both spline-base…
High-dimensional prediction considers data with more variables than samples. Generic research goals are to find the best predictor or to select variables. Results may be improved by exploiting prior information in the form of co-data, providing complementary data not on the samples, but on the variables. We consider adaptive ridge penalised generalised linear and Cox models, in which the variable specific ridge penalties are adapted to the co-data to give a priori more weight to more important variables. The R-package ecpc originally accommodated various and possibly multiple co-data sources, …
Bayesian additive regression tree (BART) models have seen increased attention in recent years as a general-purpose nonparametric modeling technique. BART combines the flexibility of modern machine learning techniques with the principled uncertainty quantification of Bayesian inference, and it has been shown to be uniquely appropriate for addressing the high-noise problems that occur commonly in many areas of science, including medicine and the social sciences. This paper introduces the SoftBart package for fitting the Soft BART algorithm of Linero and Yang (2018). In addition to improving upon…
Model selection in mixed models based on the conditional distribution is appropriate for many practical applications and has been a focus of recent statistical research. In this paper we introduce the R-package cAIC4 that allows for the computation of the conditional Akaike Information Criterion (cAIC). Computation of the conditional AIC needs to take into account the uncertainty of the random effects variance and is therefore not straightforward. We introduce a fast and stable implementation for the calculation of the cAIC for linear mixed models estimated with lme4 and additive mixed models …
The University of Hong Kong（香港大学）；Suoxinda Holdings Limited（索信达控股有限公司）
In recent years, the field of recommendation systems has attracted increasing attention to developing predictive models that provide explanations of why an item is recommended to a user. The explanations can be either obtained by post-hoc diagnostics after fitting a relatively complex model or embedded into an intrinsically interpretable model. In this paper, we propose the explainable recommendation systems based on a generalized additive model with manifest and latent interactions (GAMMLI). This model architecture is intrinsically interpretable, as it additively consists of the user and item…
The BUGS language offers a very flexible way of specifying complex statistical models for the purposes of Gibbs sampling, while its JAGS variant offers very convenient R integration via the rjags package. However, including smoothers in JAGS models can involve some quite tedious coding, especially for multivariate or adaptive smoothers. Further, if an additive smooth structure is required then some care is needed, in order to centre smooths appropriately, and to find appropriate starting values. R package mgcv implements a wide range of smoothers, all in a manner appropriate for inclusion in J…
Generalized additive models (GAMs) play an important role in modeling and understanding complex relationships in modern applied statistics. They allow for flexible, data-driven estimation of covariate effects. Yet researchers often have a priori knowledge of certain effects, which might be monotonic or periodic (cyclic) or should fulfill boundary conditions. We propose a unified framework to incorporate these constraints for both univariate and bivariate effect estimates and for varying coefficients. As the framework is based on component-wise boosting methods, variables can be selected intrin…
Generalized additive models for location, scale and shape (GAMLSS) are a flexible class of regression models that allow to model multiple parameters of a distribution function, such as the mean and the standard deviation, simultaneously. With the R package gamboostLSS, we provide a boosting method to fit these models. Variable selection and model choice are naturally available within this regularized regression framework. To introduce and illustrate the R package gamboostLSS and its infrastructure, we use a data set on stunted growth in India. In addition to the specification and application o…
Cox proportional hazards model is one of the most popular models in biomedical data analysis. There have been continuing efforts to improve the flexibility of such models for complex signal detection, for example, via additive functions. Nevertheless, the task to extend Cox additive models to accommodate high-dimensional data is nontrivial. When estimating additive functions, commonly used group sparse regularization may introduce excess smoothing shrinkage on additive functions, damaging predictive performance. Moreover, an "all-in-all-out" approach makes functional selection challenging to a…
In this article, we introduce the BNPqte R package which implements the Bayesian nonparametric approach of Xu, Daniels and Winterstein (2018) for estimating quantile treatment effects in observational studies. This approach provides flexible modeling of the distributions of potential outcomes, so it is capable of capturing a variety of underlying relationships among the outcomes, treatments and confounders and estimating multiple quantile treatment effects simultaneously. Specifically, this approach uses a Bayesian additive regression trees (BART) model to estimate the propensity score and a D…
Generalized additive models (GAMs) are flexible non-linear regression models, which can be fitted efficiently using the approximate Bayesian methods provided by the mgcv R package. While the GAM methods provided by mgcv are based on the assumption that the response distribution is modelled parametrically, here we discuss more flexible methods that do not entail any parametric assumption. In particular, this article introduces the qgam package, which is an extension of mgcv providing fast calibrated Bayesian methods for fitting quantile GAMs (QGAMs) in R. QGAMs are based on a smooth version of …
