All functions

add_barrier_mesh()

Transform a mesh object into a barrier mesh object

bc_coast

BC coastline data from ropensci/rnaturalearthhires

extract_mcmc()

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

Beta() lognormal() nbinom2() truncated_nbinom2() student() tweedie()

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

inla_installed()

Check if INLA installed (i.e., not on CRAN)

make_mesh() plot(<sdmTMBmesh>)

Construct an SPDE mesh for sdmTMB

make_spde() plot_spde()

Construct an SPDE mesh (depreciated)

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

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

run_extra_optimization()

Run extra optimization on an already fitted object

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

sdmTMBcontrol()

Optimization control options

tidy(<sdmTMB>)

Turn sdmTMB model output into a tidy data frame

update_model()

Update an old sdmTMB model