Man pages for jkbest2/spatq
Use spatially varying catchability to standardize fishery-dependent data
| all_res_file_paths | List paths for all result files |
| attach_optdiags | Attach optimization diagnostics |
| bias_metric | Estimate bias of estimation models |
| build_expr_str | Build an expression string from a list of string vectors |
| create_index_df | Create a data frame with index locations and times |
| dim_or_len | Get 'dim' if available, 'length' otherwise |
| domain_boundary | Define the domain boundary |
| em_estd | Estimated parameters for an estimation model |
| em_subsample | Specify data subsample for estimation model |
| field_image | Plot a field |
| fit_spatq | Fit a spatq model by maximum likelihood |
| fix_nlminb_fit | Make 'nlminb' output match 'optim' output |
| fixpar_corr | Correlation matrix of the fixed-effect parameters |
| fixpar_corrplot | Plot the fixed-effect parameter correlation matrix |
| fixpar_covcond | Calculate the condition number of the fixed-effect parameter... |
| fixpar_grad | Gradients at the fitted values |
| fixpar_highcorr | Fixed-effect parameters with high correlations |
| fixpar_mgc | Maximum gradient component at fitted parameter values |
| fixpar_sd | Return the standard deviations of the fixed-effect parameters |
| gather_nvec | Gather a named vector into a list |
| generate_aniso_fem | Generate anisotropic FEM matrices |
| generate_empty_projection | Generate an empty project matrix |
| generate_fem | Generate FEM matrices |
| generate_mesh | Generate INLA mesh |
| generate_projection | Generate a projection matrix |
| get_coordref | Read the index to coordinate reference table |
| get_index_filetype | Get index file type |
| get_newpars | Get updated parameter values |
| index_path | Construct the relative path to the index file output by a... |
| init_fixef | Initial estimates of fixed effect parameters |
| interleave_estgen | Alternate estimated and generative parameter vectors |
| is_estd_proc | Check if process is estimated |
| isgen | Is this parameter generative or estimated? |
| layout_mat | Construct layout matrix for field plots |
| loc_grid | Generate a location grid |
| make_sim_adfun | Create ADFun from simulated data |
| map_correlation | Calculate the correlation between true and estimated... |
| mgc | Maximum gradient component |
| new_spatq_setup | Set up inputs for spatq model |
| nulleigs | Find the parameters that contribute to a singular covariance... |
| par_expr | Pretty expressions for plotting parameter names |
| par_expr_parts | Strings from parameter names to be expression-ified |
| pars_data | Parameter values from data elements |
| parse_coords | Parse a tuple of numbers read as a string |
| pars_tau | The SPDE construction uses parameters kappa and tau, while... |
| plot_colorbar | Plot a colorbar legend |
| plot_field | Plot spatial and spatiotemporal fields |
| plot_popstate | Plot array of population states (simulated "truth") |
| posdefhess | Is the Hessian positive definite? |
| prepare_adfun | Make a TMB ADFun |
| prepare_data | Prepare the 'data' argument for the 'spatq' model |
| prepare_map | Prepare a 'map' |
| prepare_pars | Prepare parameter list |
| prepare_proc_switch | Prepare process switch |
| prepare_random | Prepare 'random' |
| proc_colormap | Colormaps for numbers density and weight per group fields |
| project_field | Project random effects, reshape to array |
| rdata_path | Construct the relative path to the Rdata fit file |
| read_all_indices | Load index CSVs for a study |
| read_catch | Read simulated data |
| read_catchability | Read catchability |
| read_estpop | Read and reshape population estimates |
| read_index | Read an index from a fitted model |
| read_index_csv | Read indices of abundance |
| read_popstate | Read true population state for each year |
| read_rdata | Read saved Rdata from a fitted model |
| re_par_idx | General random effects parameter index |
| repl_dir | Directory name for each replicate |
| rescale_index | Rescale indices |
| res_file_paths | Paths to each results file |
| rmse_metric | Root mean square error |
| save_fit | Save fit results |
| save_index | Save true and estimated indices to a CSV |
| sim_file_paths | Paths to simulated data sets |
| spat_par_idx | Spatial parameter index |
| spatq | Spatially varying catchability for fishery-dependent... |
| spatq_fit | Fit a spatq model by maximum likelihood |
| spatq_obj | Contstruct a spatq objective function |
| spatq_optcontrol | Control parameters for optimization |
| spatq_simsetup | Construct a spatq_setup from a simulated data set |
| spatq_simstudyspec | Simulation study specification |
| specify_estimated | Specify which parameters to estimate |
| study_dir | Directory where a study's simulations live |
| subsample_catch | Subsample catch by year |
| terminate_opt | Test whether optimization should be stopped |
| true_percentile | Percentile of true value in estimated distribution |
| update_onepar | Update a single parameter vector |
| update_setup | Update a model setup |
| verify_ident_fixef | Verify that fixed effects are identifiable |
| verify_setequal | Verify two sets are equal |
| verify_spatq | Check 'spatq' inputs |
| verify_spatq_dims | Check 'spatq' component dimensions |
| verify_spatq_map | Check that 'map' is self-consistent |
| verify_spatq_names | Check all 'spatq' components are present |
