Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

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Documentation for package ‘sdmTMB’ version 0.6.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

add_utm_columns	Add UTM coordinates to a data frame
dharma_residuals	DHARMa residuals
dogfish	Example fish survey data
Effect.sdmTMB	Calculate effects
emmeans.sdmTMB	Estimated marginal means with the 'emmeans' package with 'sdmTMB'
gather_sims	Extract parameter simulations from the joint precision matrix
get_cog	Extract a relative biomass/abundance index or a center of gravity
get_crs	Add UTM coordinates to a data frame
get_index	Extract a relative biomass/abundance index or a center of gravity
get_index_sims	Calculate a population index via simulation from the joint precision matrix
get_pars	Get TMB parameter list
halfnormal	Prior distributions
hbll_s_grid	Example fish survey data
make_mesh	Construct an SPDE mesh for sdmTMB
mvnormal	Prior distributions
normal	Prior distributions
pcod	Example fish survey data
pcod_2011	Example fish survey data
pcod_mesh_2011	Example fish survey data
pc_matern	Prior distributions
plot.sdmTMBmesh	Construct an SPDE mesh for sdmTMB
plot_anisotropy	Plot anisotropy from an sdmTMB model
plot_anisotropy2	Plot anisotropy from an sdmTMB model
plot_pc_matern	Plot PC Matérn priors
plot_smooth	Plot a smooth term from an sdmTMB model
predict.sdmTMB	Predict from an sdmTMB model
qcs_grid	Example fish survey data
replicate_df	Replicate a prediction data frame over time
residuals.sdmTMB	Residuals method for sdmTMB models
run_extra_optimization	Run extra optimization on an already fitted object
sanity	Sanity check of an sdmTMB model
sdmTMB	Fit a spatial or spatiotemporal GLMM with TMB
sdmTMBcontrol	Optimization control options
sdmTMBpriors	Prior distributions
sdmTMB_cv	Cross validation with sdmTMB models
sdmTMB_simulate	Simulate from a spatial/spatiotemporal model
sdmTMB_stacking	Perform stacking with log scores on 'sdmTMB_cv()' output
set_delta_model	Set delta model for 'ggeffects::ggpredict()'
simulate.sdmTMB	Simulate from a fitted sdmTMB model
spread_sims	Extract parameter simulations from the joint precision matrix
tidy.sdmTMB	Turn sdmTMB model output into a tidy data frame
visreg2d_delta	Plot sdmTMB models with the 'visreg' package
visreg_delta	Plot sdmTMB models with the 'visreg' package
wcvi_grid	Example fish survey data
yelloweye	Example fish survey data