Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'


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Documentation for package ‘sdmTMB’ version 0.3.0

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