sdmTMB: 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. (2024) <doi:10.1101/2022.03.24.485545>.

Version: 0.6.0
Depends: R (≥ 3.5.0)
Imports: assertthat, clisymbols, cli, fmesher, fishMod, generics, graphics, lifecycle, lme4, Matrix, methods, mgcv, mvtnorm, nlme, rlang, stats, TMB (≥ 1.8.0)
LinkingTo: RcppEigen, TMB
Suggests: DHARMa, dplyr, effects (≥ 4.0-1), estimability, emmeans (≥ 1.4), future, future.apply, ggeffects, ggforce, glmmTMB, ggplot2, knitr, rmarkdown, sf, splancs, testthat, tibble, visreg
Published: 2024-05-30
DOI: 10.32614/CRAN.package.sdmTMB
Author: Sean C. Anderson ORCID iD [aut, cre] (<https://orcid.org/0000-0001-9563-1937>), Eric J. Ward ORCID iD [aut] (<https://orcid.org/0000-0002-4359-0296>), Philina A. English ORCID iD [aut] (<https://orcid.org/0000-0003-2992-6782>), Lewis A. K. Barnett ORCID iD [aut] (<https://orcid.org/0000-0002-9381-8375>), James T. Thorson ORCID iD [aut, cph] (<https://orcid.org/0000-0001-7415-1010>, VAST author), Joe Watson [ctb] (Censored Poisson), Julia Indivero [ctb] (Vignette writing), Jillian C. Dunic ORCID iD [ctb] (<https://orcid.org/0000-0002-0729-3083>), Cole C. Monnahan ORCID iD [ctb, cph] (<https://orcid.org/0000-0003-0871-6700>, VAST contributor), Mollie Brooks ORCID iD [ctb, cph] (<https://orcid.org/0000-0001-6963-8326>, glmmTMB author), Ben Bolker ORCID iD [ctb, cph] (<https://orcid.org/0000-0002-2127-0443>, glmmTMB author), Kasper Kristensen [ctb, cph] (TMB/glmmTMB author), Martin Maechler ORCID iD [ctb, cph] (<https://orcid.org/0000-0002-8685-9910>, glmmTMB author), Arni Magnusson ORCID iD [ctb, cph] (<https://orcid.org/0000-0003-2769-6741>, glmmTMB author), Hans J. Skaug [ctb, cph] (glmmTMB author, SPDE barrier), Anders Nielsen ORCID iD [ctb, cph] (<https://orcid.org/0000-0001-9683-9262>, glmmTMB author), Casper Berg ORCID iD [ctb, cph] (<https://orcid.org/0000-0002-3812-5269>, glmmTMB author), Koen van Bentham [ctb, cph] (glmmTMB author), Olav Nikolai Breivik [ctb, cph] (SPDE barrier), Simon Wood [ctb, cph] (mgcv: smoother prediction), Paul-Christian Bürkner [ctb, cph] (brms: smoother matrix parsing), His Majesty the King in Right of Canada, as represented by the Minister of the Department of Fisheries and Oceans [cph]
Maintainer: Sean C. Anderson <sean at seananderson.ca>
BugReports: https://github.com/pbs-assess/sdmTMB/issues
License: GPL-3
Copyright: inst/COPYRIGHTS
sdmTMB copyright details
URL: https://pbs-assess.github.io/sdmTMB/, https://github.com/pbs-assess/sdmTMB
NeedsCompilation: yes
SystemRequirements: GNU make
Citation: sdmTMB citation info
Materials: NEWS
In views: SpatioTemporal
CRAN checks: sdmTMB results

Documentation:

Reference manual: sdmTMB.pdf
Vignettes: sdmTMB model description

Downloads:

Package source: sdmTMB_0.6.0.tar.gz
Windows binaries: r-devel: sdmTMB_0.6.0.zip, r-release: sdmTMB_0.6.0.zip, r-oldrel: sdmTMB_0.6.0.zip
macOS binaries: r-release (arm64): sdmTMB_0.6.0.tgz, r-oldrel (arm64): sdmTMB_0.6.0.tgz, r-release (x86_64): sdmTMB_0.6.0.tgz, r-oldrel (x86_64): sdmTMB_0.6.0.tgz
Old sources: sdmTMB archive

Reverse dependencies:

Reverse suggests: clustTMB, ggeffects

Linking:

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