Function reference

Mesh construction

Tools for converting coordinates into UTMs, constructing SPDE meshes prior to model fitting, and adding correlation barriers.

add_utm_columns() get_crs()

Add UTM coordinates to a data frame

make_mesh() plot(<sdmTMBmesh>)

Construct an SPDE mesh for sdmTMB

add_barrier_mesh()

Transform a mesh object into a mesh with correlation barriers

Fitting and predicting

Core tools for model fitting, prediction, and inspection.

sdmTMB()

Fit a spatial or spatiotemporal GLMM with TMB

predict(<sdmTMB>)

Predict from an sdmTMB model

tidy(<sdmTMB>)

Turn sdmTMB model output into a tidy data frame

sanity()

Sanity check of an sdmTMB model

sdmTMBcontrol()

Optimization control options

run_extra_optimization()

Run extra optimization on an already fitted object

residuals(<sdmTMB>)

Residuals method for sdmTMB models

dharma_residuals()

DHARMa residuals

replicate_df()

Replicate a prediction data frame over time

set_delta_model()

Set delta model for ggeffects::ggpredict()

Families

Additional families beyond the standard R families.

Beta() lognormal() gengamma() gamma_mix() lognormal_mix() nbinom2_mix() nbinom2() nbinom1() truncated_nbinom2() truncated_nbinom1() student() tweedie() censored_poisson() delta_gamma() delta_gamma_mix() delta_gengamma() delta_lognormal() delta_lognormal_mix() delta_truncated_nbinom2() delta_truncated_nbinom1() delta_poisson_link_gamma() delta_poisson_link_lognormal() delta_beta()

Additional families

Priors

Optional priors or penalties on parameters.

sdmTMBpriors() normal() halfnormal() mvnormal() pc_matern()

Prior distributions

plot_pc_matern()

Plot PC Matérn priors

Simulation

Simulating new data with an sdmTMB model.

simulate(<sdmTMB>)

Simulate from a fitted sdmTMB model

sdmTMB_simulate()

Simulate from a spatial/spatiotemporal model

Plotting

Functions for plotting.

plot_anisotropy() plot_anisotropy2()

Plot anisotropy from an sdmTMB model

plot_smooth()

Plot a smooth term from an sdmTMB model

plot_pc_matern()

Plot PC Matérn priors

visreg_delta() visreg2d_delta()

Plot sdmTMB models with the visreg package

Cross validation

Functions related to cross validation.

sdmTMB_cv()

Cross validation with sdmTMB models

sdmTMB_stacking()

Perform stacking with log scores on sdmTMB_cv() output

Derived quantities

Derived quantities that can be calculated from sdmTMB models.

get_index() get_cog()

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

Miscellaneous parameter extraction

Functions for calculating effect sizes or extracting parameter samples.

Effect.sdmTMB()

Calculate effects

emmeans.sdmTMB

Estimated marginal means with the emmeans package with sdmTMB

spread_sims() gather_sims()

Extract parameter simulations from the joint precision matrix