| add_extra_ribbon_data | Add extra data for decreasing-sized polygons which will be... |
| add_major_ticks | Create a vector of labels to use when major and minor tick... |
| add_newlines | Replace '+' with a newline in the given string |
| add_utm_columns | Add UTM coordinates to a data frame (Copied from gfplot... |
| age_bubble_cohorts | A vector of years when larger-than-normal recruitment took... |
| age_diag_linecolor | The default color to use for diagonal cohort lines on age... |
| age_diag_linetype | The default line type to use for diagonal cohort lines on age... |
| age_diag_linewidth | The default line width to use for diagonal cohort lines on... |
| age_fillcolor | The default fill color to use for bubbles in age bubble plots |
| alt_text_inject_tags | Inject the 'tagpdf' code around the figure chunk given by the... |
| assess_changes_df | A data frame containing information on changes in the... |
| assess_history_df | A data frame containing information on estimated biomass... |
| assess_history_probs_df | A data frame containing information on probability of biomass... |
| as_ts_mcmc | Coerce an MCMC object to a time series |
| axis_label_color | The color to use by default for all axis titles |
| axis_tick_font_size | The size font to use by default for all axis tick labels |
| axis_title_font_size | The size font to use by default for all axis titles |
| beta_get_shape_params | Calculate the two shape parameters from the mean ('mu') and... |
| bind_cols_quiet | Wrapper for 'dplyr::bind_cols()' but silences the New... |
| calc_ageerror | Calculate ageing error matrix |
| calc_fishery_ages | Load data and create age compositions for the fishery |
| calc_historical_probs | Calculate probabilities from an MCMC model to compare with... |
| calc_lw_params | Calculate length-weight relationship parameters |
| calc_mcmc | Return a list of mcmc calculations, e.g. quantiles for... |
| calc_mcmc_param_stats | Calculate Autocorrelation, Effective sample size, Geweke... |
| calc_quantiles | Calculate and insert columns containing arbitrary quantiles... |
| calc_refpt_quants | Calculations for the reference points table |
| calc_retro_stats | Add a new year of biomass dispersion stats to the CSV file... |
| calc_risk | Calculate the probabilities of being under several reference... |
| calc_sum_rec_devs | Calculate the men, median, and range of the recruitment... |
| calc_yoob | Calculate the data outside the range of the y limits and... |
| canada_create_age_proportions_csv | Create an age proportion CSV data from the sample data |
| canada_create_commercial_waa | create the weight-at-age CSV file for Canadian commercial... |
| canada_create_fleet_month_catch_csv_files | Create CSV files with catch by year and month for Canadian... |
| canada_create_fleet_year_catch_csv_files | Calculate the catch by year and fishery for Canadian... |
| canada_depth_sql_fn | Name of file containing the SQL code to extract Canadian... |
| canada_extract_depth_data_from_db | Extract the Canadian depth and fishing event data |
| canada_extract_fleet_catch | Merge Canadian DMP and LOGS catch data and extract into 3... |
| canada_extract_samples_from_db | Extract the Canadian biological sample data |
| canada_extract_sampling_by_month | Extract the number of age, length, and weight samples by... |
| canada_get_fleet_samples | Split up the Canadian samples data frame into fleet data... |
| canada_load_catch_data | Load Canadian catch data from files extracted using the FOS... |
| canada_load_sample_data | Load the Canadian commercial sample data |
| canada_sql_inject_fishery_filters | Inject SQL code for fishery categories and types based on the... |
| can_catch_by_year_fn | The filename for the Canadian catch by year |
| can_ft_age_df | A data frame containing information about the proportions of... |
| can_ft_age_props_fn | The filename for the Freezer trawler age proportions by year... |
| can_ft_bottom_depth_df | A data frame containing information about the depths of the... |
| can_ft_catch_by_month_df | A data frame containing catch information on Canadian Freezer... |
| can_ft_catch_by_month_fn | The filename for the Freezer trawler catch by year and month... |
| can_ft_gear_depth_df | A data frame containing information about the depths of the... |
| can_ft_num_fish | A data frame containing information about the number of fish... |
| can_jv_age_props_fn | The filename for the Joint venture age proportions by year... |
| can_jv_catch_by_month_df | A data frame containing catch information on Canadian... |
| can_jv_catch_by_month_fn | The filename for the Joint venture catch by year and month... |
| can_jv_num_fish | A data frame containing information about the number of fish... |
| can_raw_ft_age_counts_fn | The filename for the Freezer trawler raw age counts by year... |
| can_raw_jv_age_counts_fn | The filename for the Joint venture raw age counts by year... |
| can_raw_ss_age_counts_fn | The filename for the Shoreside raw age counts by year data... |
| can_sample_data_rds_fn | The filename for the RDS file containing hake sample data as... |
| can_ss_age_df | A data frame containing information about the proportions of... |
| can_ss_age_props_fn | The filename for the Shoreside age proportions by year data... |
| can_ss_bottom_depth_df | A data frame containing information about the depths of the... |
| can_ss_catch_by_month_df | A data frame containing catch information on Canadian... |
| can_ss_catch_by_month_fn | The filename for the Shoreside catch by year and month data... |
| can_ss_gear_depth_df | A data frame containing information about the depths of the... |
| can_ss_num_fish | A data frame containing information about the number of fish... |
| can_waa_fn | The filename for the Canadian weight-at-age CSV file |
| caption_adjustments_fn | Name of file containing the caption adjustments for figures... |
| catch_targets_biomass_fn | The filename for the file containing coastwide catch targets... |
| catch_targets_df | A data frame containing information on the actual catch,... |
| check_catch_levels | Check that catch levels has been run |
| check_forecasts | Check that forecasts have been run |
| clean | Clean (delete) all build output including knitr cache and... |
| clean_all | Run 'clean()' on directories used for rendering the document... |
| cohort_catch | Calculate the total catch taken for a given cohort |
| combine_historical_probs | Calculate a model's probability of stock decline in a year... |
| comp_report_fn | A character string containing the file name for the SS3 Comp... |
| compute_hexagon_xy | Compute the coordinates for a hexagon to be shown in a... |
| control_fn | A character string containing the file name for the SS3... |
| convert_ctl_file_param_dfs | Convert a control file parameter data frame into a format... |
| covar_fn | A character string containing the name of the covariance... |
| create_data_hake | Create package data with one call |
| create_depth_by_year_csv_files | Get depth data by year and calculate boxplot stats on it.... |
| create_fontsize_str | Creates a LaTeX font size string which can be used in table... |
| create_group_df_biomass | Create a data frame containing model output of biomass from a... |
| create_group_df_index | Create a data frame containing model output index fits from a... |
| create_group_df_recr | Create a data frame containing model output recruitment from... |
| create_rds_attach_forecasts | Load catch levels and forecasting and attach to as RDS file |
| create_rds_attach_retrospectives | Load retrospective RDS files and attach to as RDS file |
| create_rds_file | Create an rds file to hold the model's data and outputs. |
| create_rds_files_retro | Create the RDS files for all retrospective runs |
| create_sens_dirs | Create standard sensitivity directories |
| create_version_dirs | Create set of directories for a new model version |
| ct | A data frame containing information on catch by year and... |
| ct_levels_catch_tol | The tolerance in tonnes. The iterations will stop if the... |
| ct_levels_max_iter | The maximum number of iterations to do. If this is reached,... |
| ct_levels_path | Directory name for storing the catch levels calculations. |
| ct_levels_spr_tol | Custom catch levels calculations. The tolerance in the SPR... |
| curr_time_date | Create a time and date string for the title page of the doc |
| data_fn | A character string containing the file name for the SS3 data... |
| data_new_ssnew_fn | A character string containing the name of the secondary file... |
| data_ssnew_fn | A character string containing the name of the file SS3... |
| data_tables_path | The directory name for the directory containing the data... |
| default_hr_path | Directory name for storing the default harvest rule catch... |
| delete_dirs | Delete all directories and files of 'sub_dir" |
| delete_rds_files | Delete all model rds files found in the subdirectories of the... |
| derposts_fn | A character string containing the file name for the SS3... |
| dirclip | Copy the current working directory to the system clipboard |
| doc_path | Directory name for the main assessment document. |
| draw_arrows_yoob | Draw arrows on the top and/or bottom of the plot pointing to... |
| enact_privacy_rule | Apply the confidentiality rule to spatial data. Copied from... |
| extract_alt_text | Extract contents of text found in a '(ref:variable-alt)'... |
| extract_inline_rcode | Replace all occurrences of inline R chunks with the... |
| extract_inside_catch | Extract the inside (Strait of Georgia) hake catch by year |
| extract_label_from_figure_filename | Extract chunk label for the knitr chunk containing... |
| extract_mcmc_quant | Extract MCMC quantiles from models and return them in a... |
| extract_rep_table | Extract the vectors from a list into a 'tibble::tibble()' |
| extract_sigma_r | Extract the 'sigma_R_info' table from a data frame of... |
| extract_survey_index_fits | Extract index fit MCMC quantiles from models and return them... |
| f | Format a number |
| firstup | Convert the first letter of a string to uppercase |
| fit_lw | Fit a length-weight model |
| fix_posteriors | Remove multiple header/data rows found in posteriors files to... |
| fix_title_case_for_csl | Add an additional layer of curly braces around the titles... |
| forecast_descriptions_fn | Name of file containing the forecasting descriptions and... |
| forecast_fn | A character string containing the file name for the SS3... |
| forecasts_path | Directory name for storing the forecasting. |
| forecasts_prepend | Name to be prepended to year for forecast directory names. |
| further_tac_details_fn | The filename for the file containing further TAC details such... |
| further_tac_df | A data frame containing information on extra TAC information |
| get_age_comp_limits | Get the start and end year of the age comp data, and maximum... |
| get_age_prop | Create the age prop and the age itself for the ranking of age... |
| get_age_proportions_by_fleet | Calculates the age proportions by year and returns a list... |
| get_assess_yr | Get the current assessment year |
| get_col_name_from_key_title | Get the name of a column in the input data frame that matches... |
| get_doc_type | Get the document type for the given RMD file |
| get_key_nuisance_posts | Create the 'nuisance' and 'key' posteriors CSV files in the... |
| get_obj_sizes | Get the object sizes in bytes for elements of the input list |
| get_os | Return the Operating System name in lower case |
| get_param_est_comparison_df | Create the data frame that holds parameter estimates for... |
| get_post_cols | Extract time series columns for a given parameter and change... |
| get_posterior_data | Get the posterior values for the given regular expressions of... |
| get_prior_data | Get the prior and MLE values for the given regular... |
| get_prior_string | Looks at the prior type p_type and phase, and if uniform will... |
| get_rec_ci | Get recruitment information for a cohort from two models with... |
| get_ss3_exe_name | Get the name of the SS3 executable to use. |
| get_year_range | Get best start year and end year values given the data... |
| goback | Navigate back to the directory you were in before calling... |
| gotest | Create and change to a temporary directory and copy a... |
| gotest_beamer_get_src_dest_filenames | Create the lists of source and destination filenames needed... |
| gotest_doc_get_src_dest_filenames | Create the lists of source and destination filenames needed... |
| group_test_models | Group the input list of models into a list of sub-lists of... |
| hake | hake: A package for creating the Pacific hake stock... |
| hake_beamer | Custom function to allow the post processing steps to be run... |
| hake_pdf | Custom function to allow the post processing steps to be run... |
| hake_theme | Theme for the 'ggplot2::ggplot()' plots in the document |
| heatmap_add_extrap_yrs_wa | Add extrapolated years before and after the weight-at-age... |
| heatmap_calc_function | Calculate values for a given range of years, for ages which... |
| heatmap_extract_sample_size | Extract the sample size data frame, or a data frame of... |
| heatmap_get_wa_ggplot_vals | Get a data frame which is subset of a data frame used by... |
| heatmap_set_colors | Ramp colors given to the length of the number of ages in the... |
| hex_coords | A cleaned-up copy of hexbins::hexcoords() |
| insert_row | Insert a new row made up of the vector 'row_vec' at row... |
| key_posteriors | A list of key posteriors for this assessment |
| key_posteriors_fn | A character string containing the file name for the key... |
| key_posteriors_titles | A list of key posterior names for this assessment |
| kriging_pars_df | A data frame containing information about the Kriging... |
| landings_tac_fn | The filename for the landings and TAC history for the US and... |
| large_cohorts | A vector of years when larger-than-normal recruitment took... |
| latex_amp | Create a string with 'n' ampersands separated by spaces |
| latex_bold | Wrap the given text with the latex \textbf macro around it |
| latex_cline | Provide latex code to draw a horizontal line across the... |
| latex_italics | Wrap the given text with the latex \emph macro around it |
| latex_mcol | Wrap the given text with the latex \multicolumnn macro around... |
| latex_size_str | Creates a string which has the given font size and space size... |
| latex_subscr | Creates a latex string with 'main_txt' subscripted by... |
| latex_under | Wrap the given text with the latex \underline macro around it |
| linebreaker | Place a LaTeX \\makecell{} macro around some text |
| load_all_models_in_subdir | Load all models from a directory with subdirectories |
| load_can_age_data | Load the Canadian age data from the CSV file which contains... |
| load_ct_levels | Load catch levels from SS forecast files. |
| load_extra_mcmc | Create and return a list of output stats to attach to the... |
| load_extra_mcmc_age_comps | Load the age composition estimates from the extra MCMC output |
| load_extra_mcmc_atage | Load at-age data chunks from a list of report file output,... |
| load_extra_mcmc_biomass | Load the biomass outputs from the extra MCMC output |
| load_extra_mcmc_get_chunk | Extracts a vector of lines of data or output (a chunk) from... |
| load_extra_mcmc_get_parameter_chunk | Extracts a vector of lines of data or output (a chunk) from... |
| load_extra_mcmc_init_nage | Load the inital numbers-at-age as defined in... |
| load_extra_mcmc_m | Load the natural mortality outputs from the extra MCMC output |
| load_extra_mcmc_recr_cohorts | Load the recruitment outputs from the extra MCMC output for... |
| load_extra_mcmc_recr_devs | Load the inital numbers-at-age as defined in... |
| load_extra_mcmc_repfiles | Load all SS3 report files from the directory provided and... |
| load_forecasts | Fetch the output from previously-run forecasting using... |
| load_mcmc_vals | Load some values from the MCMC output and store in a list |
| load_parameter_priors | Load values (priors) from the 'parameters' data frame in the... |
| load_ss_files | Load all the SS files for output and input, and return the... |
| main_alpha | The transparency to use by default for all fills in the plots... |
| main_fill | The color to use by default for all fills in the plots in the... |
| make_major_tick_labels | Create a vector of x-axis tick labels by only populating the... |
| maturity_estimates_df | A data frame containing information on the maturity estimates... |
| maturity_samples_df | A data frame containing information on ovary sampling |
| mcmc_path | Directory name for the mcmc output for models |
| minor_tick_length | The length of the minor tick marks in plots in cm |
| model_output_log_fn | A character string containing the file name for the model... |
| model_setup | Load models and set up lists and classes for the base model,... |
| modify_starter_mcmc_type | Change the MCMC setting in an SS starter file so the extra... |
| mutsel | Link together 'dplyr::mutate()' and 'dplyr::select()' |
| nuisance_posteriors_fn | A character string containing the file name for the nuisance... |
| number_to_word | Change a number into an English word |
| object_placement_fn | Name of file containing the object placement settings for... |
| obj_sizes | Return a data frame of the names and sizes of the objects in... |
| ordered_decision_table_paths | An ordered vector of the paths used in the decision table for... |
| out_csv_path | Directory name for outputting the CSV versions of at-age... |
| output_permissions | The Linux file permissions value to use for fs::file_chmod() |
| ovary_samples_df | A data frame containing information on ovary sampling |
| pacea_save | Save some results as '.rds' files to then be imported into... |
| pad_num | Pad the beginning of numbers in a vector with zeroes so they... |
| pad_weight_at_age | Fill in necessary years of weight-at-age file |
| par_fn | A character string containing the file name for the SS3 par... |
| plot_age_comp_bubbles | Make an age composition bubble plot |
| plot_age_comp_bubbles_data | Create a multi-panel plot of age proportion bubble plots, one... |
| plot_age_comp_comparison_bubbles | Create a plot of age proportions as bubbles with fishery and... |
| plot_age_comp_fit | Create a set of barplots by year with the bars being observed... |
| plot_assessment_history_biomass | Title |
| plot_assessment_history_disp | Create Interquartile range or quartile coefficient of... |
| plot_assessment_timeline | Create a plot showing the relative numbers of days we have... |
| plot_autocor | Create an autocorrelation plot for a particular parameter |
| plot_biomass | Plot biomass from MCMC output for one or more models.... |
| plot_biomass_fished_unfished | Plot the fished biomass vs. the unfished biomass for a model |
| plot_bubbles | Make a bubble plot from the given data |
| plot_catchability_density | Plot the density histogram for the posteriors for... |
| plot_catch_by_month | Create a plot of cumulative catches, with one panel for each... |
| plot_catches | Plot catch data as a stacked barplot |
| plot_color | Colors for the Hake Assessment |
| plot_comparison | Create an n-panel plot of the biomass, relative biomass, or... |
| plot_cumulative_catch_cohorts | Creates a plot showing the cumulative catches for certain... |
| plot_data_summary | Create a plot with three panels showing a summary of the data... |
| plot_density | Create a density plot for a particular parameter |
| plot_depth | Create a boxplot of depths for a given data frame |
| plot_depth_2_panel | Create a 2-panel plot with fishing depth on the left and... |
| plot_depth_4_panel | Create a 4-panel plot with fishing depth on the left and... |
| plot_during_loading | Create plots during the loading phase, and return a list of... |
| plot_fecundity | Create a aplot of fecundity-at-age and mean-weight-at-age |
| plot_fore_age_comps | Create a two-panel plot showing the forecasted age... |
| plot_heatmap_sample_size_weight_at_age | Create a weight-at-age heatmap including extrapolated years |
| plot_heatmap_weight_at_age | Create a weight-at-age heatmap including extrapolated years |
| plot_historical_probs | Plots to compare historical and current probabilities |
| plot_historical_probs_retro | Make individual plots (or one overlaid) of historical... |
| plot_intensity_illustration | Create a plot illustrating the fishing intensity as a... |
| plot_management_catch_vs_tac | Make a time series plot of the management-chosen TAC,... |
| plot_management_catch_vs_tac_1_to_1 | Plot the TAC vs realized catch on a 1-to-1 plot |
| plot_map | Create a map of a part of the west coast of North America,... |
| plot_maturity_ogives | Create a plot containing the maturity ogives by year on a... |
| plot_mcmc_diagnostics | Plot MCMC diagnostics |
| plot_mcmc_diagnostics_all_params | Creates the plot showing the 4 MCMC diagnostics for all... |
| plot_mcmc_histogram | Plot a histogram for a given column in a data frame |
| plot_overview_map | Create a map of the west coast of North America showing... |
| plot_pairs | Create a pairs plot showing correlations among key parameters... |
| plot_param_density | Create a plot showing the density of the posterior for the... |
| plot_pearson_bubbles | Make a bubble plot from the given data |
| plot_phase | Create plot of the relative fishing intensity in year t-1... |
| plot_priors_vs_posts | Make a grid of posterior plots with priors and initial values |
| plot_retro_recruits | Make squid plot of retrospectives of recruitment deviations. |
| plot_retro_yrs | The years previous to the end of the time series to include... |
| plot_running_quants | Create a plot with running quantiles across the posterior for... |
| plot_selex_mountains | Create a plot of median selectivity as a set of overlapping... |
| plot_selex_posteriors | Plot the selectivity parameter estimates from all posteriors... |
| plot_selex_uncertainty | Create a plot of time-varying selectivity panels |
| plot_spatial_cpue | Create a map of the west coast of North America showing... |
| plot_spr_illustration | Create a three-panel plot illustrating how the SPR is... |
| plot_squid | Make the retrospective recruitment deviations plot (squid... |
| plot_stock_recruitment | Create a plot of the stock-recruitment relationship with... |
| plot_survey_biomass | Create a plot of survey biomass as points with error bars |
| plot_survey_fit_mcmc | Creates a plot of fits to survey biomass including individual... |
| plot_trace | Create a trace plot for a particular parameter |
| plot_weight_at_age | Create a plot of weight-at-age lines by age and year |
| plot_weights_lengths | Plot some years of weight of length histograms |
| ports_df | A data frame containing information about the ports used in... |
| post_process | Post-process the TEX file output by Bookdown |
| post_process_add_alt_text | Add alternative text to figures in the document via the... |
| post_process_add_appendix_counter_resets | Add appendix counter rests LaTeX code for equations, figures,... |
| post_process_add_counters | Add LaTeX counter code so that the Executive summary has... |
| post_process_add_headers_footers | Add left and right footer text to the pages |
| post_process_add_horiz_lines_decision_table | Adds two horizontal lines to the decision tables |
| post_process_add_picture_to_title_page | Insert an image on the title page |
| post_process_add_start_appendices_code | Add start appendices LaTeX code |
| post_process_add_vert_space_after_header | Add LaTeX vertical space code after the Executive Summary... |
| post_process_beamer | Post-process the TEX file output by Bookdown for beamer... |
| post_process_beamer_add_extra_headers_etc | Add extra headers needed for tables, colors in tables,... |
| post_process_beamer_insert_disclaimer | Insert a disclaimer notice at the bottom of the title page of... |
| post_process_beamer_insert_title_page_logos | Insert the NOAA and DFO logos and a hake picture on the title... |
| post_process_beamer_make_title_page_plain | Remove theme shadow and navigation bar from the title page |
| post_process_convert_section_headers | Replace chapter with section for all sections, and prepend a... |
| post_process_error_check | Check the input LaTex for errors or omissions before post... |
| post_process_extract_chunks | Extract chunks of lines from a vector of lines |
| post_process_fix_landscape_issues | Remove landscape/portrait code between tables/figures which... |
| post_process_fix_tildes | Change tildes (~) so that they will make it through the... |
| post_process_interlace_chunks | Interlace chunks of code that have been extracted by... |
| post_process_landscape_figures | Post-process landscape figures in TEX code |
| post_process_landscape_tables | Post-process landscape tables in TEX code |
| post_process_longtables | Post-process LaTeX longtables in TEX code |
| post_process_modify_font_info | Modify the font type and size in the LaTeX code |
| post_process_modify_link_colors | Modify reference link colors in the document |
| post_process_move_table_captions | Move certain table captions, usually to left-justify. There... |
| post_process_object_placement | Modify the tex code 'x' by changing the table or figure label... |
| post_process_remove_title_page_number | Removes the page number from the title page |
| post_process_repair_unnumbered_section_links | Add phantomsection tag to sections that are unnumbered to... |
| post_process_set_latex_placement_options | Inject LaTeX float placement codes for figure and tables,... |
| post_process_table_of_contents | Insert the table of contents into TeX code |
| posts_fn | A character string containing the file name for the SS3... |
| probs | A vector of the probabilities to use for uncertainty... |
| probs_forecast | A vector of the probabilities to use for uncertainty... |
| psv_fn | A character string containing the file name for the SS3 psv... |
| rbeta_ab | The Beta distribution |
| read_bookdown_file | Read a _bookdown.yml file into a reasonable format which is a... |
| recruit_dev_start_yr | The year in which the recruitment deviations start in the... |
| refpt_bo_linecolor | The color of the horizontal line representing B0 |
| refpt_bo_linetype | The default line type to use for the horizontal line... |
| refpt_bo_linewidth | The default line width to use for the horizontal line... |
| refpt_lrp_linecolor | The color of the horizontal line representing the limit... |
| refpt_lrp_linetype | The default line type to use for the horizontal line... |
| refpt_lrp_linewidth | The default line width to use for the horizontal line... |
| refpt_usr_linecolor | The color of the horizontal line representing the upper stock... |
| refpt_usr_linetype | The default line type to use for the horizontal line... |
| refpt_usr_linewidth | The default line width to use for the horizontal line... |
| regex_eml_recdevs | Regular expression for the "early", "main", and "late"... |
| regex_extra_mcmc_compreport | Regular expression for the CompReport files in the extra MCMC... |
| regex_extra_mcmc_report | Regular expression for the Report files in the extra MCMC... |
| regex_main_recdevs | Regular expression for the "main" recruitment deviation... |
| regex_recdev_all | Regular expression for the "early", "main", and "late"... |
| regex_recdev_early | Regular expression for the "early initial" (Early_InitAge)... |
| remove_forecast_outputs | Remove the 'outputs' list item from the 'catch_levels' lists... |
| render | Render the Hake assessment document PDF file |
| replace_dotted_paths | Replace dotted paths in the vector with their correct full... |
| report_fn | A character string containing the file name for the SS3... |
| retropectives_path | Directory name for storing the retrospectives. |
| retrospectives_prepend | Name to be prepended to year for retrospective directory... |
| retrospective_yrs | The years previous to the end of the time series to strip off... |
| rich_colors_short | Create rich colors as RGB strings |
| run_adnuts | Run the adnuts MCMC for the model found in the directory... |
| run_adnuts_timed | Run 'run_adnuts()' with a timer |
| run_catch_levels_copy_input_files | Copy the necessary files from a models' work directories to... |
| run_ct_levels | A wrapper to run the catch levels determination routines |
| run_ct_levels_default_hr | Run the model, iteratively reducing the difference between... |
| run_ct_levels_spr_100 | Run the model iteratively zoning in on a catch value that... |
| run_ct_levels_stable_catch | Run the model iteratively reducing the difference between the... |
| run_extra_forecasts | Run extra forecasting for the model supplied |
| run_forecasts | Run forecasting for a model in parallel when possible |
| run_retrospectives | Runs retrospectives for the given model and for the vector of... |
| sampling_history_df | A data frame containing information on amount of sampling... |
| save_nuts_fits | Read in NUTS run data files ('hake.Rdata' files), fix the... |
| set_ct_levels | Reads in the forecast description data and creates the list... |
| set_dirs | Set and return all model directories for the project |
| show_ss_output | A character string containing the name of the variable flag... |
| split_prior_info | Extract priors information from a string with a particular... |
| spr_100_path | Directory name for storing the SPR 100 catch levels |
| sql_path | Directory name for any SQL code files |
| ss_executable | A character string containing the name of the SS3 executable... |
| ss_input_files | A vector of character strings containing the file names... |
| sso_path | Directory name for the mcmc output when MCMC_output_detail in... |
| stable_catch_path | Directory name for storing the stable catch catch levels |
| starter_fn | A character string containing the file name for the SS3... |
| start_yr | The starting year for the model estimates |
| start_yr_age_comps | The starting year for the age composition data in the model |
| states_df | A data frame containing information about the states and... |
| stop_quietly | Stop the program without issuing an error message |
| survey_end_yr | The last year for the acoustic survey in the model |
| survey_history_df | A data frame containing information about the history of all... |
| survey_start_yr | The starting year for the acoustic survey in the model |
| surv_yrs | A vector of years in which the acoustic survey took place and... |
| system_ | Call 'shell()' or 'system()' depending on the Operating... |
| table_above_avg_cohorts_yrs | Create a table containing some years' estimated recruitment... |
| table_age_data | Creates a table containing single-fleet age proportions which... |
| table_assessment_changes | Title |
| table_at_age | Makes a table of the estimated -at-age values for 5 different... |
| table_biomass | Create a table of spawning biomass and relative spawning... |
| table_catch | Create a table of total catch |
| table_catch_by_fleet | Create a table containing the catch-at-age for one of the 3... |
| table_catch_tac_summary | Create a table of US vs Canadian catch, TAC, and attainment... |
| table_ci_posteriors | Make a latex table of credible intervals with columns for... |
| table_cohort | Create a table of cohort biomass and natural mortality as... |
| table_decision | Create the Executive Summary decision tables. 'rows_to_label'... |
| table_decision_original | Create the Executive Summary decision tables. 'rows_to_label'... |
| table_fishing_intensity | Create a table of fishing intensity and exploitation fraction... |
| table_fore_age_props | Creates a table showing the forecast age comp percentages by... |
| table_input_age_data | Creates a table containing the age data which are input into... |
| table_landings_tac | Create a summary table of landings and TACS |
| table_maturity_ogive | Create a table containing the maturiy ogive data as input... |
| table_median_posteriors | Make a latex table of medians with columns for female... |
| table_ovary_samples | Create a table containing the ovary sampling information |
| table_param_est | Returns a 'kableExtra::kbl()' containing a comparison of... |
| table_param_est_last_year_hardcoded | Returns a 'kableExtra::kbl()' containing a comparison of... |
| table_parameters_long_summary | Title |
| table_recruitment | Create a table of absolute recruitment and relative spawning... |
| table_reference_points | Creates a table containing reference point estimates |
| table_risk | Creates LaTeX code to make a probability of risk table with... |
| table_sampling_by_month | Extract the number of samples by fleet and month for a given... |
| table_sampling_history | Creates a table of the sampling history for hake |
| table_survey_by_country | Create a table of values of the age 2+ survey biomass... |
| table_survey_history | Create a table of the acoustic survey history |
| table_yearly_model_compare | Create a table comparing this year's biomass estimate and... |
| top_coh | Create text describing the top 'num_cohorts' cohorts by year... |
| ts_linegap | The gap between the lines connecting the median points in the... |
| ts_linewidth | The line width to use for the line connecting the median... |
| ts_pointshape | The point shape to use for the medians in the time series... |
| ts_pointsize | The point size to use for the medians in the time series... |
| ts_pointstroke | The point stroke (boldness) to use for the points... |
| ts_ribbon_alpha | The transparency to use by default to fill time series CI... |
| ts_ribbon_linetype | The line type for the edges of the CI ribbon for time series... |
| ts_single_model_linecolor | The line color to use for the line connecting the median... |
| ts_single_model_linetype | The line type to use for the line connecting the median... |
| ts_single_model_linewidth | The line width to use for the line connecting the median... |
| ts_single_model_pointcolor | The point color to use for the median points in the time... |
| ts_single_model_pointshape | The point shape to use for the points representing the median... |
| ts_single_model_pointsize | The point size to use for the points representing the median... |
| ts_single_model_pointstroke | The point stroke (boldness) to use for the points... |
| ts_single_model_ribbon_fill | The color to use to fill time series CI ribbons for plots... |
| ts_single_model_ribbon_linetype | The line type to use for the borders on the CI ribbons for... |
| unfished_eq_yr | The year in which unfished equilibrium is set |
| update_ss3_ageing_error | Insert ageing error matrix if needed |
| update_ss3_catch | Update the catches in a Stock Synthesis file |
| update_ss3_maturity | Update maturity in an SS3 weight-at-age matrix |
| us_atsea_bottom_depth_df | A data frame containing information about the depths of the... |
| us_atsea_fishing_depth_df | A data frame containing information about the depths of the... |
| us_cp_age_df | A data frame containing information about the proportions of... |
| us_cp_age_props_fn | The filename for the Catcher-processor fleet age proportions... |
| us_cp_catch_by_month_df | A data frame containing catch information on U.S.... |
| us_cp_prop_tac | The proportion of the U.S. TAC that the Catcher-processor... |
| us_extract_sampling_by_month | Extract the number of ages, lengths, and weights month for... |
| us_ms_age_df | A data frame containing information about the proportions of... |
| us_ms_age_props_fn | The filename for the U.S. Mothership fleet age proportions by... |
| us_ms_catch_by_month_df | A data frame containing catch information on U.S. ti vessels... |
| us_ms_prop_tac | The proportion of the U.S. TAC that the Mothership sector... |
| us_research_catch_by_month_df | A data frame containing catch information on U.S. research... |
| us_sb_age_props_fn | The filename for the U.S. Shore-based fleet age proportions... |
| us_ss_age_df | A data frame containing information about the proportions of... |
| us_ss_catch_by_month_df | A data frame containing catch information on U.S. shore-based... |
| us_ss_prop_tac | The proportion of the U.S. TAC that the Shore-based sector... |
| us_ti_ct_by_month_df | A data frame containing catch information on U.S. tribal... |
| utils_update_catch_sums | Updates the most recent catch time values stored in... |
| vec2df | Create a one-row data frame from a vector of values |
| weight_age_sample_sizes_df | A data frame containing information on weight-at-age |
| weight_at_age_fn | A character string containing the file name for the SS3... |
| yaml_check_margin_format | Check the format of the margin command entered into the YAML... |
