Package: sdmTMB 0.6.0.9021

Sean C. Anderson

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>.

Authors:Sean C. Anderson [aut, cre], Eric J. Ward [aut], Philina A. English [aut], Lewis A. K. Barnett [aut], James T. Thorson [aut, cph], Joe Watson [ctb], Julia Indivero [ctb], Jillian C. Dunic [ctb], Cole C. Monnahan [ctb, cph], Mollie Brooks [ctb, cph], Ben Bolker [ctb, cph], Kasper Kristensen [ctb, cph], Martin Maechler [ctb, cph], Arni Magnusson [ctb, cph], Hans J. Skaug [ctb, cph], Anders Nielsen [ctb, cph], Casper Berg [ctb, cph], Koen van Bentham [ctb, cph], Olav Nikolai Breivik [ctb, cph], Simon Wood [ctb, cph], Paul-Christian Bürkner [ctb, cph], His Majesty the King in Right of Canada, as represented by the Minister of the Department of Fisheries and Oceans [cph]

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sdmTMB.pdf |sdmTMB.html✨
sdmTMB/json (API)
NEWS

# Install 'sdmTMB' in R:
install.packages('sdmTMB', repos = c('https://pbs-assess.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pbs-assess/sdmtmb/issues

Pkgdown site:https://pbs-assess.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

ecologyglmmspatial-analysisspecies-distribution-modellingtmbcpp

10.68 score 192 stars 880 scripts 1.4k downloads 60 exports 46 dependencies

Last updated 5 days agofrom:b448278d1a. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 13 2025
R-4.5-win-x86_64OKJan 13 2025
R-4.5-linux-x86_64OKJan 13 2025
R-4.4-win-x86_64OKJan 13 2025
R-4.4-mac-x86_64OKJan 13 2025
R-4.4-mac-aarch64OKJan 13 2025
R-4.3-win-x86_64OKJan 13 2025
R-4.3-mac-x86_64OKJan 13 2025
R-4.3-mac-aarch64OKJan 13 2025

Exports:add_barrier_meshadd_utm_columnsBetacAICcensored_poissondelta_betadelta_gammadelta_gamma_mixdelta_gengammadelta_lognormaldelta_lognormal_mixdelta_poisson_link_gammadelta_poisson_link_lognormaldelta_truncated_nbinom1delta_truncated_nbinom2dharma_residualsextract_mcmcgamma_mixgather_simsgengammaget_cogget_crsget_eaoget_indexget_index_simsget_parsggplot2_installedhalfnormallognormallognormal_mixmake_meshmvnormalnbinom1nbinom2nbinom2_mixnormalpc_maternplot_anisotropyplot_anisotropy2plot_pc_maternplot_smoothprojectreplicate_dfrun_extra_optimizationsanitysdmTMBsdmTMB_cvsdmTMB_simulatesdmTMB_stackingsdmTMBcontrolsdmTMBpriorsset_delta_modelspread_simsstudenttidytruncated_nbinom1truncated_nbinom2tweedievisreg_deltavisreg2d_delta

Dependencies:abindassertthatbootclassclassIntcliDBIdplyre1071fansifishModfmeshergenericsglueKernSmoothlatticelifecyclelme4magrittrMASSMatrixmgcvminqamvtnormnlmenloptrpillarpkgconfigproxyR6rbibutilsRcppRcppEigenRdpackreformulasrlangs2sftibbletidyselectTMBunitsutf8vctrswithrwk

sdmTMB model description

Rendered frommodel-description.Rmdusingknitr::rmarkdownon Jan 13 2025.

Last update: 2024-06-12
Started: 2020-10-05

Readme and manuals

Help Manual

Help pageTopics
Add UTM coordinates to a data frameadd_utm_columns get_crs
Calculate conditional AICcAIC
Get fixed-effect coefficientscoef.sdmTMB
DHARMa residualsdharma_residuals
Calculate effectsEffect.sdmTMB
Estimated marginal means with the 'emmeans' package with 'sdmTMB'emmeans.sdmTMB
Extract a relative biomass/abundance index, center of gravity, or effective area occupiedget_cog get_eao get_index
Calculate a population index via simulation from the joint precision matrixget_index_sims
Get TMB parameter listget_pars
Construct an SPDE mesh for sdmTMBmake_mesh plot.sdmTMBmesh
Example fish survey datadogfish hbll_s_grid pcod pcod_2011 pcod_mesh_2011 qcs_grid wcvi_grid yelloweye
Plot anisotropy from an sdmTMB modelplot_anisotropy plot_anisotropy2
Plot PC Matérn priorsplot_pc_matern
Plot a smooth term from an sdmTMB modelplot_smooth
Predict from an sdmTMB modelpredict.sdmTMB
Project from an 'sdmTMB' model using simulationproject
Replicate a prediction data frame over timereplicate_df
Residuals method for sdmTMB modelsresiduals.sdmTMB
Run extra optimization on an already fitted objectrun_extra_optimization
Sanity check of an sdmTMB modelsanity
Fit a spatial or spatiotemporal GLMM with TMBsdmTMB
Cross validation with sdmTMB modelssdmTMB_cv
Simulate from a spatial/spatiotemporal modelsdmTMB_simulate
Perform stacking with log scores on 'sdmTMB_cv()' outputsdmTMB_stacking
Optimization control optionssdmTMBcontrol
Prior distributionshalfnormal mvnormal normal pc_matern sdmTMBpriors
Set delta model for 'ggeffects::ggpredict()'set_delta_model
Simulate from a fitted sdmTMB modelsimulate.sdmTMB
Extract parameter simulations from the joint precision matrixgather_sims spread_sims
Turn sdmTMB model output into a tidy data frametidy.sdmTMB
Plot sdmTMB models with the 'visreg' packagevisreg2d_delta visreg_delta