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Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'
Implements spatial and spatiotemporal GLMMs (Generalized Linear
Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial
Differential Equation) Gaussian Markov random field approximation to
Gaussian random fields. One common application is for spatially explicit
species distribution models (SDMs).
See Anderson et al. (2025)
Suite of Deterministic and Robust Algorithms for Linear Regression
DetLTS, DetMM (and DetS) Algorithms for Deterministic, Robust Linear Regression.
Facilities for Simulating from ODE-Based Models
Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.
R Package Installation from Remote Repositories, Including 'GitHub'
Download and install R packages stored in 'GitHub', 'GitLab', 'Bitbucket', 'Bioconductor', or plain 'subversion' or 'git' repositories. This package provides the 'install_*' functions in 'devtools'. Indeed most of the code was copied over from 'devtools'.
Multinomial Logit Models for Categorical Responses and Discrete Choices
Provides estimators for multinomial logit models in their conditional logit (for discrete choices) and baseline logit variants (for categorical responses), optionally with overdispersion or random effects. Random effects models are estimated using the PQL technique (based on a Laplace approximation) or the MQL technique (based on a Solomon-Cox approximation). Estimates should be treated with caution if the group sizes are small.
Animated Interactive Grammar of Graphics
Functions are provided for defining animated,
interactive data visualizations in R code, and rendering
on a web page. The 2018 Journal of Computational and
Graphical Statistics paper,
Tools for Developing R Packages Interfacing with 'Stan'
Provides various tools for developers of R packages interfacing with 'Stan' < https://mc-stan.org>, including functions to set up the required package structure, S3 generics and default methods to unify function naming across 'Stan'-based R packages, and vignettes with recommendations for developers.
Access the Bioconductor Project Package Repository
A convenient tool to install and update Bioconductor packages.
Bayesian Additive Regression Trees with Stan-Sampled Parametric Extensions
Fits semiparametric linear and multilevel models with non-parametric additive Bayesian additive regression tree (BART; Chipman, George, and McCulloch (2010)
Define and Work with Parameter Spaces for Complex Algorithms
Define parameter spaces, constraints and dependencies for arbitrary algorithms, to program on such spaces. Also includes statistical designs and random samplers. Objects are implemented as 'R6' classes.