Man pages for James-Thorson/VAST
Vector-Autoregressive Spatio-Temporal (VAST) Model
| amend_output | Amend output from VAST for user convenience |
| apply_epsilon | Custom epsilon-correct method |
| arrowtooth_trends | Data to demonstrate and test decadal-trends model |
| bilinear_interp | Plot vessel effects |
| Build_TMB_Fn | Copy of VAST::make_model |
| Calc_Anisotropic_Mesh | Copy of make_mesh |
| calc_coherence | Calculate stability metrics |
| calc_cov | Calculate covariance |
| Calc_Polygon_Areas_and_Polygons_Fn | Copy of calculate_knot_areas |
| calc_synchrony | Calculate synchrony among species or locations |
| calculate_knot_areas | Calculate areas and covariates for a given triangulated mesh |
| calculate_proportion | Calculate the compositional-expansion |
| check_fit | Check fit for VAST model |
| Coherence | Calculate stability metrics |
| combine_extrapolation_info | Combines multiple extrapolation grids |
| combine_lists | Combine lists |
| Convert_LL_to_EastNorth_Fn | Convert from Lat-Long to Eastings-Northings using WGS |
| Convert_LL_to_UTM_Fn | Convert from Lat-Long to UTM |
| convert_shapefile | Convert shapefile to extrapolation-grid |
| convert_version_name | Convert string to semantic version number |
| Crossvalidate_Fn | K-fold crossvalidation |
| Data_Fn | Copy of VAST::make_data |
| Effect.fit_model | Adapts package 'effects' |
| fit_model | Fit VAST to data |
| fit_tmb | Optimize a TMB model |
| format_covariates | Format habitat covariate matrix |
| Geostat_Sim | Simulate data |
| get_latest_version | Determine latest version of VAST |
| GOA_pcod_covariate_example | Data to demonstrate and test covariate effects |
| goa_traits | Data to demonstrate and test trait-based multispeces SDM |
| list_parameters | List fixed and random effects |
| load_example | Load an example data set |
| make_covariates | Format density covariate matrix |
| make_data | Build data input for VAST model |
| make_extrapolation_info | Build extrapolation grid |
| make_kmeans | Calculate location for knots approximating spatial variation |
| make_map | Create a tagged list to turn and off and mirror parameters |
| make_map_info | Get information for adequate mapping for regions |
| make_mesh | Make mesh for distances among points |
| make_model | Build TMB object for VAST model |
| make_parameters | Calculate parameter inputs for TMB |
| make_settings | Make list of settings |
| make_spatial_info | Build objects related to spatial information |
| map_hypervariance | Plot variance of GMRF knots |
| oneStepPredict_deltaModel | Calculate one-step-ahead (OSA) residuals for a mixed-effects... |
| Param_Fn | Copy of make_parameters |
| plot_anisotropy | Plot geometric anisotropy |
| plot_biomass_index | Plot index of abundance |
| plot_clusters | Plot spatial clusters |
| plot_cov | Plot covariance matrix |
| plot_data | Plot location of sampling data |
| plot_dharma | Plot DHARMa residuals |
| plot_encounter_diagnostic | Check predicted encounter probability against observed... |
| Plot_factors | Copy of plot_factors |
| plot.fit_model | Print parameter estimates |
| plot_index | Plot an index |
| plot_legend | Plot standard maps |
| plot_loadings | Plotting loadings matrix |
| plot.make_extrapolation_info | Plot extrapolation-grid |
| plot.make_spatial_info | Plot spatial information |
| PlotMap_Fn | Plot maps with areal results |
| plot_maps | Plot standard maps |
| Plot_Overdispersion | Copy of plot_overdispersion |
| plot_quantile_diagnostic | Diagnostic QQ function |
| plot_quantile_residuals | Plot quantile residuals on map |
| plot_range_edge | Plot shifts in range edges |
| plot_range_index | Plot shifts in distribution and area occupied |
| plot_residuals | Plot Pearson residuals on map |
| plot_residual_semivariance | Plot semivariance for quantile residuals |
| plot_results | Plot results |
| plot_similarity | Plot similarity resulting from estimated covariance |
| plot_timeseries | Plot timeseries estimates |
| plot_variable | Plot results on a multi-panel figure of maps |
| pollock_cohorts | Data to demonstrate and test cohort effects in age-structured... |
| predict.fit_model | Predict density for new samples (_Beta version; may change... |
| print.fit_model | Print parameter estimates |
| print.make_data | Print data |
| print.make_extrapolation_info | Extract extrapolation-grid |
| print.make_model | Print model object |
| print.make_spatial_info | Print spatial information |
| project_coordinates | Convert from Lat-Long to UTM |
| project_model | Project a fitted VAST model forward in time |
| reload_model | Reload a VAST model |
| Rerun_Fn | Explore counter-factual scenario |
| rotate_factors | Rotate results |
| sample_variable | Sample from predictive distribution of a variable |
| simulate_data | Simulate new dynamics and sampling data |
| smallPlot | Inset small plot within figure |
| stream_network_eel_example | Data to demonstrate and test stream-network options |
| strip_units | Remove units from object |
| Summarize_Covariance | Copy of summarize_covariance |
| summary.fit_model | Extract summary of spatial estimates |
| TMBAIC | Calculate marginal AIC for a fitted model |
| VAST | Vector Autoregressive Spatio-Temporal Model |
