Man pages for iantaylor-NOAA/Lingcod_2021
Estimate the Status of Lingcod off the US West Coast in 2021
| add_data | Add data to lingcod model |
| add_figure_ling | Add a data frame of figures. |
| add_figure_vast | Write a csv file of figures for a given VAST index |
| change_ages | Switch between conditional (CAAL) and marginal age for a... |
| change_control_fleets | renumber fleets in lingcod control file |
| change_data_fleets | renumber fleets in lingcod data file |
| change_pars | change parameter values in a table within the control file... |
| clean_comps | change the column names in the data.frame of length or age... |
| coef_year | Get model coefficients for year |
| compile_changebookname | Change bookname in the _bookdown.yml file |
| compile_internal | A non-vectorized version of compile |
| compile_ling | Compile the stock assessment document(s) for a given species |
| cpue_output | Read in OR index table information |
| create_caal_nonsurvey | Generate CAAL compositions from any dataset |
| data_catch | Model catches |
| data_index_cpue | Index for catch per unit effort (CPUE) |
| data_index_survey | Index for the standardized surveys |
| dir_order | Order a vector of files based on their manipulation time. |
| dir_recent | Find the most recent file in a directory that matches the... |
| discard_rates_combined | Combine discard rates from multiple sources |
| file_local | Find a file specific to the lingcod package |
| format_range | Format text for a range from a vector |
| get_dir_exe | Get directory with Stock Synthesis executable in Lingcod... |
| get_dir_ling | get directory for a lingcod model |
| get_fleet | translate between fleet names and numbers and old or new |
| get_groups | Get grouping structure for a given species |
| get_id_ling | get id for a lingcod model from the directory |
| get_inputs_ling | get SS input files for a lingcod model |
| get_mdtable | Get a markdown table from within a section in a .md file |
| get_mod | get directory for a lingcod model |
| get_SS_prior | get prior values for prior types and parameterizations used... |
| get_year | Get the assessment year |
| ggsave2 | Save a ggplot2::ggplot figure with caption and alt text |
| info_areacolors | Area colors |
| info_authors | A list of authors used for writing the assessment(s) |
| info_basemodels | Base model folder names |
| info_bins | A list of bins used for composition data |
| info_groups | A data frame of groups used to structure output and the... |
| info_surveynames | Names of included surveys |
| install_clone | Install the cloned version of a repository in R |
| kable_captioncontinue | Create a caption for a longtable that is continued |
| kable_styling_sa4ss | Formatting for a long table with repeated headers |
| last_ssdat | Last assessment's SS dat files |
| last_ssdir | Last assessment's model directory |
| make_r4ss_plots_ling | Make r4ss plots for Lingcod assessment |
| mult_lbs2mt | Converter to get from pounds to metric tons |
| pipe | Pipe operator |
| plot_indices | Plot all indices in one figure for the lingcod models |
| plot_map | Plot a map of the states with data using ggplot2::ggplot |
| plot_north_vs_south | Make a series of plots comparing the north and south modnels |
| plot_ntable | Plot sample sizes by group horizontally |
| plot_rec_selectivity_illustration | Make a figure to illustrate rec catch |
| plot_sel_comm | Plot selectivity and retention for the commercial fleets |
| plot_sel_noncomm | Plot selectivity and retention for the non-commercial fleets |
| plot_sel_ret | Plot time-varying selectivity or selectivity |
| plot_stock_boundary_map | Plot a map of the stock boundaries for the 2021 lingcod... |
| plot_theme | Plot themes for ggplot2::ggplot figures |
| plot_twopanel_comparison | Plot a two-panel comparison using SSplotComparisons |
| plot_VASTresiduals | Plot VAST residuals |
| ref_goodlabel | Format a vector of labels for markdown |
| ref_range | Reference a range of figure numbers |
| run_investigatemodel | Run all model investigations for a base model |
| run_lorenzenm | Run a model using Lorenzen natural mortality |
| run_regularization | Example script to run MCMC using R package adnuts for SS |
| run_sensitivities | Run sensitivities for a base model |
| run_vast | Run VAST for a single survey |
| sens_clean_labels | create a nicer label for model output tables |
| sens_convert_offsets | convert parameter offsets to standard space |
| sens_convert_vals | Convert offset parameters |
| sens_make_table | Make a table of senstivity results |
| setup_areastrata | Create a data frame of stratifications for each area |
| SS_readdat.list | Read in a multiple SS dat files from directories into a list |
| string_switchletter | Switch a single letter in a string with a new letter |
| survey_acomps | Expand the age-composition data for a given survey |
| survey_lcomps | Expand the length-composition data for a given survey |
| table_compweight | Table of parameters |
| table_decision | Format a decision table |
| table_dq | Table of likelihoods by source |
| table_likelihoods | Table of likelihoods by source |
| table_outputconfig | Summarize the configuration of the SS output |
| table_pars | Table of parameters |
| table_profile | Summarize profile results of parameters |
| table_projections | Table of projections |
| table_sens | Summarize the configuration of the SS output |
| table_ts | Table of estimated time series |
| use_fleetabb | Get fleet abbreviation based on gear group |
| utils_knit_opts | Set up knitr options |
| utils_name | Get name |
| write_custom_plots_csv | Write a CSV file for custom plots |
| write_draft | Write the draft assessment files for this species |
| write_inputs_ling | write SS input files for a lingcod model |
| write_introduction | Write the introduction file |
