All functions

add_barrier_mesh()

Transform a mesh object into a barrier mesh object

add_utm_columns() get_crs()

Add UTM coordinates to a data frame

bc_coast

BC coastline data from ropensci/rnaturalearthhires

dharma_residuals()

Get DHARMa residuals

extract_mcmc()

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

Beta() lognormal() nbinom2() nbinom1() truncated_nbinom2() truncated_nbinom1() student() tweedie() censored_poisson() delta_gamma() delta_lognormal() delta_truncated_nbinom2() delta_truncated_nbinom1() delta_poisson_link_gamma()

Additional families

spread_sims() gather_sims()

Extract parameter simulations from the joint precision matrix

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

make_mesh() plot(<sdmTMBmesh>)

Construct an SPDE mesh for sdmTMB

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)

plot_anisotropy()

Plot anisotropy

plot_pc_matern()

Plot PC Matern priors

plot_smooth()

Plot a smooth term from an sdmTMB model

predict(<sdmTMB>)

Predict from an sdmTMB model

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

Prior distributions

qcs_grid

Example 2x2km prediction grid for Queen Charlotte Sound

residuals(<sdmTMB>)

Residuals method for sdmTMB models

run_extra_optimization()

Run extra optimization on an already fitted object

sanity()

Sanity check of sdmTMB model

sdmTMB()

Fit a spatial or spatiotemporal GLMM with TMB

sdmTMB_cv()

Save log likelihoods of k-fold cross-validation for sdmTMB models

sdmTMB_sim()

Simulate from a spatial/spatiotemporal model

sdmTMB_simulate()

Simulate from a spatial/spatiotemporal model

sdmTMB_stacking()

Perform stacking with log scores on sdmTMB_cv() output

sdmTMBcontrol()

Optimization control options

simulate(<sdmTMB>)

Simulate from a fitted sdmTMB model

tidy(<sdmTMB>)

Turn sdmTMB model output into a tidy data frame

visreg_delta() visreg2d_delta()

Plot sdmTMB models with the visreg package