Man pages for pbs-assess/herringutils
Provides Plotting, Table-making, and Utility Functions for the CSAS Herring Documents
| add_cols_and_reorder | Add missing columns with names in 'by' not in the column... |
| basic_table | General table for the herring assessment. |
| consecutive_group | Function to add a new column indicating group ID based on... |
| decision_tables_mp | Make decision table based on MP data |
| get_catch | Summarize catch by region and gear |
| get_hcr_tac_hr | Calculate median of the TAC and HR from the hcr.lst |
| get_vars | Get model output values for a given region. |
| hcr | Return the appropriate HCR values for the given 'row' as it... |
| hcr.min.esc | Calculate TAC and TAC-based harvest rate based on a minimum... |
| hcr.ref.pts | Calculate TAC and TAC-based harvest rate based on biomass... |
| input_data_table | Table showing input data to the herring assessment. |
| mean_harvest_text | Text for "Application of MPs.." section. |
| modify_axes_labels | Add or omit the x and y label and tick mark text to a ggplot. |
| newline_format | Insert a newline between words so that all single lines will... |
| plot_bh | Plot Beverton-holt |
| plot_biomass_catch | Plot estimated biommass median and credible interval,... |
| plot_biomass_phase | Plot production using a phase plot with a path through time.... |
| plot_biomass_total_biomass | Plot total and spawning biomass |
| plot_catch | Plot catch from a data frames as extracted from iscam data... |
| plot_coastwide_biomass_catch | Plot coastwide spawning biomass and catch |
| plot_harvest_rate | Effective harvest rate plot |
| plot_hcr | Plot Harvest control rules as pairs plots |
| plot_ic | Plot incidental catch from a data frame |
| plot_natural_mortality | Plot natural mortality mcmc median and credibility interval |
| plot_pa | Plot proportions-at-age time series from a data frames as... |
| plot_pa_by_gear | Plot proportions-at-age time series by gear type |
| plot_proj_biomass_density | Plot density of MCMC posterior for projected biomass with... |
| plot_recruitment | Plot recruitment as points and errorbars |
| plot_recruitment_devs | Plot recruitment deviations as points and errorbars, with a... |
| plot_scaled_abundance | ———————- Plot the median SSB as a line, with... |
| plot_spawn_ind | Plot survey indices from data frames as extracted from iscam... |
| plot_spawn_section | Plot spawn index or scaled abundance by section |
| plot_wa | Plot weight-at-age time series from a data frames as... |
| plot_wa_by_gear | Plot weight-at-age time series from a data frames as... |
| prod_period_table | Table showing productive period and related information |
| proj_biomass_text | Text for "Application of MPs.." section. |
| sok_harvest_table | Table for the Spawn on kelp harvest for herring |
| spawn_index_by_area_table | Table for spawn index by area |
| spawn_index_table | Table for the spawn index in multiple areas |
| stock_status_text | Text for "Stock status update" section. |
| total_landed_catch_table | Table showing the total landed catch by area for herring |
