add_utm_columns |
Add UTM coordinates to a data frame |
dharma_residuals |
DHARMa residuals |
dogfish |
Example fish survey data |
Effect.sdmTMB |
Calculate effects |
emmeans.sdmTMB |
Estimated marginal means with the 'emmeans' package with 'sdmTMB' |
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 |
hbll_s_grid |
Example fish survey data |
make_mesh |
Construct an SPDE mesh for sdmTMB |
mvnormal |
Prior distributions |
normal |
Prior distributions |
pcod |
Example fish survey data |
pcod_2011 |
Example fish survey data |
pcod_mesh_2011 |
Example fish survey data |
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 fish survey data |
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 |
set_delta_model |
Set delta model for 'ggeffects::ggpredict()' |
simulate.sdmTMB |
Simulate from a fitted sdmTMB model |
spread_sims |
Extract parameter simulations from the joint precision matrix |
tidy.sdmTMB |
Turn sdmTMB model output into a tidy data frame |
visreg2d_delta |
Plot sdmTMB models with the 'visreg' package |
visreg_delta |
Plot sdmTMB models with the 'visreg' package |
wcvi_grid |
Example fish survey data |
yelloweye |
Example fish survey data |