Package index • sdmTMBexperiments

Model selection

sdmTMB_selection(): Compare a set of sdmTMB model-selection candidates
selection_frame(): Complete-case frame for a set of model-selection candidates
best_candidate(): The best candidate in a selection table
add_aic_weights(): Add delta-AIC and Akaike weights to a comparison table
sdmTMB_cv_summary(): Summarise an sdmTMB cross-validation on a per-observation scale

compare_models(): Compare sdmTMB models
compare_meshes(): Compare survey indices across different mesh cutoff values
sdmTMB_mesh_cv(): Spatial cross-validation across mesh cutoff values

compare_surveys(): Compare individual survey indices to a compiled sdmTMB index
survey_spec(): Define a survey for compare_surveys()

sdmTMB_leave_out(): Leave-one-out influence of surveys, cruises or hauls on an sdmTMB index
density_share(): Share of each haul or cruise in the annual summed density
sdmTMB_data_scenarios(): Refit an sdmTMB index under alternative data filters
peak_ratio(): Ratio of an index value to its neighbouring years
index_by_region(): Split a gridded index by region

make_survey_prediction_region(): Build a concave-hull prediction region from survey positions
make_prediction_grid(): Build a regular prediction grid over a region

plot_mesh(): Plot an sdmTMB mesh on a map
plot_prediction_map(): Map predicted densities from an sdmTMB model
plot_random_field(): Map spatial or spatiotemporal random fields
plot_index(): Plot an sdmTMB survey index
plot_fixed_effects(): Coefficient plot of sdmTMB fixed effects
plot_variance_partitioning(): Variance partitioning of an sdmTMB model
plot_prediction_histogram(): Histograms of observed and predicted response
plot_residual_qq(): Quantile-quantile plot of sdmTMB randomized quantile residuals
bubble_map(): Bubble map of a response variable
plot(<sdmTMB_data_scenarios>): Plot data-filter scenarios
plot(<sdmTMB_leave_out>): Plot leave-one-out influence
plot(<sdmTMB_mesh_comparison>): Plot mesh comparison results
plot(<sdmTMB_mesh_cv>): Plot mesh cross-validation results
plot(<sdmTMB_model_comparison>): Plot sdmTMB model comparison results
plot(<sdmTMB_prediction_grid>): Plot a prediction grid on a map
plot(<sdmTMB_region_index>): Plot an index split by region
plot(<sdmTMB_retro>): Plot retrospective indices from sdmTMB_retro
plot(<sdmTMB_selection>): Plot an sdmTMB selection table
plot(<sdmTMB_survey_comparison>): Plot survey comparison results

sebastes: Beaked redfish survey stations (example data)
sebastes_bathy: Coarse bathymetry for the example data (demonstration only)
sebastes_depth(): Depth lookup from the bundled demonstration bathymetry