Resources

General

Bolker et al. 2021: GLMM FAQ

Wikle et al. 2019: Spatio-Temporal Statistics with R

Model Validation

Tutorials and Examples

DHARMa: residual diagnostics for hierarchical (multi-level/mixed) regression models

Validation chapter in TMB documentation

Key literature

Dunn and Smyth 1996

Thygesen et al. 2017

TMB (Template Model Builder)

The comprehensive TMB documentation

Tutorials and Examples

glmmTMB: Generalized Linear Mixed Models using Template Model Builder

Key literature

Brooks et al. 2017

Kristensen et al. 2016

Monnahan and Kristensen 2018

Osgood-Zimmerman and Wakefield 2021

INLA

R-INLA website

INLA source code

Tutorials and Examples

List of useful links from r-inla.org

Introduction to INLA for geospatial modelling

Intro to modeling using INLA

INLA mesh test

A primer on crashing INLA models

Key literature

Bachl et al. 2019

Blangiardo and Cameletti 2015

Gómez-Rubio 2020

Harvard and Rue 2015

Krainski et al. 2019

Lindegren and Rue 2015

Lindegren et al. 2011

Rue et al. 2009

Example applications

Anderson and Ward 2019 - extremes

Anderson et al. 2019 - synopsis of fishery monitoring data

Barnett et al. 2021 - spatially explicit temporal trends

Breivik et al. 2021 - extrapolation to unobserved areas

Commander et al. 2022 - sensitivity to model choices

English et al. 2022 - climate velocity

Latimer et al. 2009 - invasive species

Rufener et al. 2021 - combining data types

Shelton et al. 2014 - comparison of performance to design-based measures of abundance and distribution

Thorson and Barnett 2017 - multivariate models

Thorson 2019 - guidance on a variety of applications in ecological assessments