sdmTMB | R package for spatial and spatiotemporal GLMMs

sdmTMB is a R library. sdmTMB has no bugs, it has no vulnerabilities and it has low support. You can download it from GitHub.

Analyzing geostatistical data (coordinate-referenced observations from some underlying spatial process) is becoming increasingly common in ecology. sdmTMB implements geostatistical spatial and spatiotemporal GLMMs using TMB for model fitting and R-INLA to set up SPDE (stochastic partial differential equation) matrices. One common application is for species distribution models (SDMs), hence the package name. The goal of sdmTMB is to provide a fast, flexible, and user-friendly interface—similar to the popular R package glmmTMB—but with a focus on spatial and spatiotemporal models with an SPDE approach. We extend the generalized linear mixed models (GLMMs) familiar to ecologists to include the following optional features:. Estimation is performed in sdmTMB via maximum marginal likelihood with the objective function calculated in TMB and minimized in R via stats::nlminb() with the random effects integrated over via the Laplace approximation. The sdmTMB package also allows for models to be passed to Stan via tmbstan, allowing for Bayesian model estimation. See ?sdmTMB and ?predict.sdmTMB for the most complete examples. Also see the vignettes (‘Articles’) on the documentation site.