# Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

## Documentation for package ‘sdmTMB’ version 1.0.0

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

## Help Pages

add_utm_columns | Add UTM coordinates to a data frame
cAIC | Calculate conditional AIC
coef.sdmTMB | Get fixed-effect coefficients
cv_to_waywiser | Convert 'sdmTMB_cv()' objects to 'sf' format for spatial assessment with 'waywiser'
dharma_residuals | DHARMa residuals
dogfish | Example fish survey data
Effect.sdmTMB | Calculate effects
emmeans.sdmTMB | Estimated marginal means with the 'emmeans' package with 'sdmTMB'
gamma_cv | Prior distributions
gather_sims | Extract parameter simulations from the joint precision matrix
get_cog | Extract a relative biomass/abundance index, center of gravity, effective area occupied, or weighted average
get_crs | Add UTM coordinates to a data frame
get_eao | Extract a relative biomass/abundance index, center of gravity, effective area occupied, or weighted average
get_index | Extract a relative biomass/abundance index, center of gravity, effective area occupied, or weighted average
get_index_sims | Calculate a population index via simulation from the joint precision matrix
get_index_split | Extract a relative biomass/abundance index, center of gravity, effective area occupied, or weighted average
get_pars | Get TMB parameter list
get_range_edge | Calculate range edges via simulation from the joint precision matrix
get_weighted_average | Extract a relative biomass/abundance index, center of gravity, effective area occupied, or weighted average
halfnormal | Prior distributions
hbll_s_grid | Example fish survey data
make_category_svc | Set up spatially varying coefficients for category composition models
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
project | Project from an 'sdmTMB' model using simulation
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()'
sigma.sdmTMB | Extract residual standard deviation or dispersion parameter
simulate.sdmTMB | Simulate from a fitted sdmTMB model
simulate_new | Simulate from a spatial/spatiotemporal model
spread_sims | Extract parameter simulations from the joint precision matrix
tidy.sdmTMB | Turn sdmTMB model output into a tidy data frame
tidy.sdmTMB_cv | Turn sdmTMB model output into a tidy data frame
update.sdmTMB | Update an sdmTMB model
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