Function reference • sdmTMB

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 sdmTMB model

sdmTMBcontrol(): Optimization control options

run_extra_optimization(): Run extra optimization on an already fitted object

fitted(<sdmTMB>): Get fitted values from an sdmTMB model

residuals(<sdmTMB>): Residuals method for sdmTMB models

dharma_residuals(): Get DHARMa residuals

Families

Additional families beyond the standard R families.

Priors

Optional priors or penalties on parameters.

sdmTMBpriors() normal() halfnormal() mvnormal() pc_matern(): Prior distributions

plot_pc_matern(): Plot PC Matern 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 Matern 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

extract_mcmc(): Extract MCMC samples from a model fit with tmbstan::tmbstan().

spread_sims() gather_sims(): Extract parameter simulations from the joint precision matrix