Additive Mixed Meta-Analysis with Spline Meta-Regression

Fit additive mixed meta-analysis (AMMA) models, extending the 'mixmeta' package < https://cran.r-project.org/package=mixmeta> to allow for spline-based meta-regression. Functions combine features of 'mgcv' < https://cran.r-project.org/package=mgcv> for building spline components and 'mixmeta' for estimating general mixed-effects meta-analysis models.

Visualisations for Generalized Additive Models

Extension of the 'mgcv' package, providing visual tools for Generalized Additive Models that exploit the additive structure of such models, scale to large data sets and can be used in conjunction with a wide range of response distributions. The focus is providing visual methods for better understanding the model output and for aiding model checking and development beyond simple exponential family regression. The graphical framework is based on the layering system provided by 'ggplot2'.

Discrete Prolate Spheroidal (Slepian) Sequence Regression Smoothers

Interface for creation of 'slp' class smoother objects for use in Generalized Additive Models (as implemented by packages 'gam' and 'mgcv').

Censored Regression with Smooth Terms

Implementation of Tobit type I and type II families for censored regression using the 'mgcv' package, based on methods detailed in Woods (2016) .

Tidy Prediction and Plotting of Generalised Additive Models

Provides functions that compute predictions from Generalised Additive Models (GAMs) fitted with 'mgcv' and return them as a tibble. These can be plotted with a generic plot()-method that uses 'ggplot2' or plotted as any other data frame. The main function is predict_gam().

Hierarchical Partitioning of Adjusted R2 and Explained Deviance for Generalized Additive Models

Conducts hierarchical partitioning to calculate individual contributions of each predictor towards adjusted R2 and explained deviance for generalized additive models based on output of 'gam()' and 'bam()' in 'mgcv' package, applying the algorithm in this paper: Lai(2024) .

Generalized Additive Models with Hyper Column

An interactive HTML widget of the perspective plot for generalized additive models. An alternative solution of the function mgcv::vis.gam(). The author has retired from academic research. Accordingly, this package should not be considered a validated tool for use in peer-reviewed publications or as the basis for grant applications.

Item-by-Item Iterative Model Fitting

Models high-dimensional data, such as RNA-seq or proteomic data using an item-by-item strategy. The package contains functions to wrap high-dimensional data and iterate over them using established R packages for regression modelling (e.g., 'glmmTMB' or 'mgcv').

Penalized Splines Mixed-Effects Models

Fit penalized splines mixed-effects models (a special case of additive models) for large longitudinal datasets. The package includes a psme() function that (1) relies on package 'mgcv' for constructing population and subject smooth functions as penalized splines, (2) transforms the constructed additive model to a linear mixed-effects model, (3) exploits package 'lme4' for model estimation and (4) backtransforms the estimated linear mixed-effects model to the additive model for interpretation and visualization. See Pedersen et al. (2019) and Bates et al. (2015) for an introduction. Unlike the gamm() function in 'mgcv', the psme() function is fast and memory-efficient, able to handle datasets with millions of observations.

Estimate Spatial Population Indices from Ecological Abundance Data

Compute relative or absolute population trends across space and time using predictions from models fitted to ecological population abundance data, as described in Knape (2025) . The package supports models fitted by 'mgcv' or 'brms', and draws from posterior predictive distributions.