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

## Documentation for package ‘sdmTMB’ version 0.3.0

- DESCRIPTION file.
- Package NEWS.

## Help Pages

add_barrier_mesh | Transform a mesh object into a mesh with correlation barriers
add_utm_columns | Add UTM coordinates to a data frame
bc_coast | BC coastline data from ropensci/rnaturalearthhires
Beta | Additional families
censored_poisson | Additional families
delta_beta | Additional families
delta_gamma | Additional families
delta_gamma_mix | Additional families
delta_lognormal | Additional families
delta_lognormal_mix | Additional families
delta_poisson_link_gamma | Additional families
delta_poisson_link_lognormal | Additional families
delta_truncated_nbinom1 | Additional families
delta_truncated_nbinom2 | Additional families
Effect.sdmTMB | Calculate effects
emmeans.sdmTMB | Estimated marginal means with the 'emmeans' package with 'sdmTMB'
Families | Additional families
gamma_mix | Additional families
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
lognormal | Additional families
lognormal_mix | Additional families
make_mesh | Construct an SPDE mesh for sdmTMB
mvnormal | Prior distributions
nbinom1 | Additional families
nbinom2 | Additional families
normal | Prior distributions
pcod | Example data for Pacific Cod
pcod_2011 | Example data for Pacific Cod (years 2011 and after)
pcod_mesh_2011 | Example SPDE mesh for the Pacific Cod data (years 2011 and after)
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 2x2km prediction grid for Queen Charlotte Sound
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
simulate.sdmTMB | Simulate from a fitted sdmTMB model
spread_sims | Extract parameter simulations from the joint precision matrix
student | Additional families
tidy.sdmTMB | Turn sdmTMB model output into a tidy data frame
truncated_nbinom1 | Additional families
truncated_nbinom2 | Additional families
tweedie | Additional families
visreg2d_delta | Plot sdmTMB models with the 'visreg' package
visreg_delta | Plot sdmTMB models with the 'visreg' package