Man pages for pacific-hake/hake-assessment
Stock Assessment for Pacific Hake

add_extra_ribbon_dataAdd extra data for decreasing-sized polygons which will be...
add_major_ticksCreate a vector of labels to use when major and minor tick...
add_newlinesReplace '+' with a newline in the given string
add_utm_columnsAdd UTM coordinates to a data frame (Copied from gfplot...
age_bubble_cohortsA vector of years when larger-than-normal recruitment took...
age_diag_linecolorThe default color to use for diagonal cohort lines on age...
age_diag_linetypeThe default line type to use for diagonal cohort lines on age...
age_diag_linewidthThe default line width to use for diagonal cohort lines on...
age_fillcolorThe default fill color to use for bubbles in age bubble plots
alt_text_inject_tagsInject the 'tagpdf' code around the figure chunk given by the...
assess_changes_dfA data frame containing information on changes in the...
assess_history_dfA data frame containing information on estimated biomass...
assess_history_probs_dfA data frame containing information on probability of biomass...
as_ts_mcmcCoerce an MCMC object to a time series
axis_label_colorThe color to use by default for all axis titles
axis_tick_font_sizeThe size font to use by default for all axis tick labels
axis_title_font_sizeThe size font to use by default for all axis titles
beta_get_shape_paramsCalculate the two shape parameters from the mean ('mu') and...
bind_cols_quietWrapper for 'dplyr::bind_cols()' but silences the New...
calc_ageerrorCalculate ageing error matrix
calc_fishery_agesLoad data and create age compositions for the fishery
calc_historical_probsCalculate probabilities from an MCMC model to compare with...
calc_lw_paramsCalculate length-weight relationship parameters
calc_mcmcReturn a list of mcmc calculations, e.g. quantiles for...
calc_mcmc_param_statsCalculate Autocorrelation, Effective sample size, Geweke...
calc_quantilesCalculate and insert columns containing arbitrary quantiles...
calc_refpt_quantsCalculations for the reference points table
calc_retro_statsAdd a new year of biomass dispersion stats to the CSV file...
calc_riskCalculate the probabilities of being under several reference...
calc_sum_rec_devsCalculate the men, median, and range of the recruitment...
calc_yoobCalculate the data outside the range of the y limits and...
canada_create_age_proportions_csvCreate an age proportion CSV data from the sample data
canada_create_commercial_waacreate the weight-at-age CSV file for Canadian commercial...
canada_create_fleet_month_catch_csv_filesCreate CSV files with catch by year and month for Canadian...
canada_create_fleet_year_catch_csv_filesCalculate the catch by year and fishery for Canadian...
canada_depth_sql_fnName of file containing the SQL code to extract Canadian...
canada_extract_depth_data_from_dbExtract the Canadian depth and fishing event data
canada_extract_fleet_catchMerge Canadian DMP and LOGS catch data and extract into 3...
canada_extract_samples_from_dbExtract the Canadian biological sample data
canada_extract_sampling_by_monthExtract the number of age, length, and weight samples by...
canada_get_fleet_samplesSplit up the Canadian samples data frame into fleet data...
canada_load_catch_dataLoad Canadian catch data from files extracted using the FOS...
canada_load_sample_dataLoad the Canadian commercial sample data
canada_sql_inject_fishery_filtersInject SQL code for fishery categories and types based on the...
can_catch_by_year_fnThe filename for the Canadian catch by year
can_ft_age_dfA data frame containing information about the proportions of...
can_ft_age_props_fnThe filename for the Freezer trawler age proportions by year...
can_ft_bottom_depth_dfA data frame containing information about the depths of the...
can_ft_catch_by_month_dfA data frame containing catch information on Canadian Freezer...
can_ft_catch_by_month_fnThe filename for the Freezer trawler catch by year and month...
can_ft_gear_depth_dfA data frame containing information about the depths of the...
can_ft_num_fishA data frame containing information about the number of fish...
can_jv_age_props_fnThe filename for the Joint venture age proportions by year...
can_jv_catch_by_month_dfA data frame containing catch information on Canadian...
can_jv_catch_by_month_fnThe filename for the Joint venture catch by year and month...
can_jv_num_fishA data frame containing information about the number of fish...
can_raw_ft_age_counts_fnThe filename for the Freezer trawler raw age counts by year...
can_raw_jv_age_counts_fnThe filename for the Joint venture raw age counts by year...
can_raw_ss_age_counts_fnThe filename for the Shoreside raw age counts by year data...
can_sample_data_rds_fnThe filename for the RDS file containing hake sample data as...
can_ss_age_dfA data frame containing information about the proportions of...
can_ss_age_props_fnThe filename for the Shoreside age proportions by year data...
can_ss_bottom_depth_dfA data frame containing information about the depths of the...
can_ss_catch_by_month_dfA data frame containing catch information on Canadian...
can_ss_catch_by_month_fnThe filename for the Shoreside catch by year and month data...
can_ss_gear_depth_dfA data frame containing information about the depths of the...
can_ss_num_fishA data frame containing information about the number of fish...
can_waa_fnThe filename for the Canadian weight-at-age CSV file
caption_adjustments_fnName of file containing the caption adjustments for figures...
catch_targets_biomass_fnThe filename for the file containing coastwide catch targets...
catch_targets_dfA data frame containing information on the actual catch,...
check_catch_levelsCheck that catch levels has been run
check_forecastsCheck that forecasts have been run
cleanClean (delete) all build output including knitr cache and...
clean_allRun 'clean()' on directories used for rendering the document...
cohort_catchCalculate the total catch taken for a given cohort
combine_historical_probsCalculate a model's probability of stock decline in a year...
comp_report_fnA character string containing the file name for the SS3 Comp...
compute_hexagon_xyCompute the coordinates for a hexagon to be shown in a...
control_fnA character string containing the file name for the SS3...
convert_ctl_file_param_dfsConvert a control file parameter data frame into a format...
covar_fnA character string containing the name of the covariance...
create_data_hakeCreate package data with one call
create_depth_by_year_csv_filesGet depth data by year and calculate boxplot stats on it....
create_fontsize_strCreates a LaTeX font size string which can be used in table...
create_group_df_biomassCreate a data frame containing model output of biomass from a...
create_group_df_indexCreate a data frame containing model output index fits from a...
create_group_df_recrCreate a data frame containing model output recruitment from...
create_rds_attach_forecastsLoad catch levels and forecasting and attach to as RDS file
create_rds_attach_retrospectivesLoad retrospective RDS files and attach to as RDS file
create_rds_fileCreate an rds file to hold the model's data and outputs.
create_rds_files_retroCreate the RDS files for all retrospective runs
create_sens_dirsCreate standard sensitivity directories
create_version_dirsCreate set of directories for a new model version
ctA data frame containing information on catch by year and...
ct_levels_catch_tolThe tolerance in tonnes. The iterations will stop if the...
ct_levels_max_iterThe maximum number of iterations to do. If this is reached,...
ct_levels_pathDirectory name for storing the catch levels calculations.
ct_levels_spr_tolCustom catch levels calculations. The tolerance in the SPR...
curr_time_dateCreate a time and date string for the title page of the doc
data_fnA character string containing the file name for the SS3 data...
data_new_ssnew_fnA character string containing the name of the secondary file...
data_ssnew_fnA character string containing the name of the file SS3...
data_tables_pathThe directory name for the directory containing the data...
default_hr_pathDirectory name for storing the default harvest rule catch...
delete_dirsDelete all directories and files of 'sub_dir"
delete_rds_filesDelete all model rds files found in the subdirectories of the...
derposts_fnA character string containing the file name for the SS3...
dirclipCopy the current working directory to the system clipboard
doc_pathDirectory name for the main assessment document.
draw_arrows_yoobDraw arrows on the top and/or bottom of the plot pointing to...
enact_privacy_ruleApply the confidentiality rule to spatial data. Copied from...
extract_alt_textExtract contents of text found in a '(ref:variable-alt)'...
extract_inline_rcodeReplace all occurrences of inline R chunks with the...
extract_inside_catchExtract the inside (Strait of Georgia) hake catch by year
extract_label_from_figure_filenameExtract chunk label for the knitr chunk containing...
extract_mcmc_quantExtract MCMC quantiles from models and return them in a...
extract_rep_tableExtract the vectors from a list into a 'tibble::tibble()'
extract_sigma_rExtract the 'sigma_R_info' table from a data frame of...
extract_survey_index_fitsExtract index fit MCMC quantiles from models and return them...
fFormat a number
firstupConvert the first letter of a string to uppercase
fit_lwFit a length-weight model
fix_posteriorsRemove multiple header/data rows found in posteriors files to...
fix_title_case_for_cslAdd an additional layer of curly braces around the titles...
forecast_descriptions_fnName of file containing the forecasting descriptions and...
forecast_fnA character string containing the file name for the SS3...
forecasts_pathDirectory name for storing the forecasting.
forecasts_prependName to be prepended to year for forecast directory names.
further_tac_details_fnThe filename for the file containing further TAC details such...
further_tac_dfA data frame containing information on extra TAC information
get_age_comp_limitsGet the start and end year of the age comp data, and maximum...
get_age_propCreate the age prop and the age itself for the ranking of age...
get_age_proportions_by_fleetCalculates the age proportions by year and returns a list...
get_assess_yrGet the current assessment year
get_col_name_from_key_titleGet the name of a column in the input data frame that matches...
get_doc_typeGet the document type for the given RMD file
get_key_nuisance_postsCreate the 'nuisance' and 'key' posteriors CSV files in the...
get_obj_sizesGet the object sizes in bytes for elements of the input list
get_osReturn the Operating System name in lower case
get_param_est_comparison_dfCreate the data frame that holds parameter estimates for...
get_post_colsExtract time series columns for a given parameter and change...
get_posterior_dataGet the posterior values for the given regular expressions of...
get_prior_dataGet the prior and MLE values for the given regular...
get_prior_stringLooks at the prior type p_type and phase, and if uniform will...
get_rec_ciGet recruitment information for a cohort from two models with...
get_ss3_exe_nameGet the name of the SS3 executable to use.
get_year_rangeGet best start year and end year values given the data...
gobackNavigate back to the directory you were in before calling...
gotestCreate and change to a temporary directory and copy a...
gotest_beamer_get_src_dest_filenamesCreate the lists of source and destination filenames needed...
gotest_doc_get_src_dest_filenamesCreate the lists of source and destination filenames needed...
group_test_modelsGroup the input list of models into a list of sub-lists of...
hakehake: A package for creating the Pacific hake stock...
hake_beamerCustom function to allow the post processing steps to be run...
hake_pdfCustom function to allow the post processing steps to be run...
hake_themeTheme for the 'ggplot2::ggplot()' plots in the document
heatmap_add_extrap_yrs_waAdd extrapolated years before and after the weight-at-age...
heatmap_calc_functionCalculate values for a given range of years, for ages which...
heatmap_extract_sample_sizeExtract the sample size data frame, or a data frame of...
heatmap_get_wa_ggplot_valsGet a data frame which is subset of a data frame used by...
heatmap_set_colorsRamp colors given to the length of the number of ages in the...
hex_coordsA cleaned-up copy of hexbins::hexcoords()
insert_rowInsert a new row made up of the vector 'row_vec' at row...
key_posteriorsA list of key posteriors for this assessment
key_posteriors_fnA character string containing the file name for the key...
key_posteriors_titlesA list of key posterior names for this assessment
kriging_pars_dfA data frame containing information about the Kriging...
landings_tac_fnThe filename for the landings and TAC history for the US and...
large_cohortsA vector of years when larger-than-normal recruitment took...
latex_ampCreate a string with 'n' ampersands separated by spaces
latex_boldWrap the given text with the latex \textbf macro around it
latex_clineProvide latex code to draw a horizontal line across the...
latex_italicsWrap the given text with the latex \emph macro around it
latex_mcolWrap the given text with the latex \multicolumnn macro around...
latex_size_strCreates a string which has the given font size and space size...
latex_subscrCreates a latex string with 'main_txt' subscripted by...
latex_underWrap the given text with the latex \underline macro around it
linebreakerPlace a LaTeX \\makecell{} macro around some text
load_all_models_in_subdirLoad all models from a directory with subdirectories
load_can_age_dataLoad the Canadian age data from the CSV file which contains...
load_ct_levelsLoad catch levels from SS forecast files.
load_extra_mcmcCreate and return a list of output stats to attach to the...
load_extra_mcmc_age_compsLoad the age composition estimates from the extra MCMC output
load_extra_mcmc_atageLoad at-age data chunks from a list of report file output,...
load_extra_mcmc_biomassLoad the biomass outputs from the extra MCMC output
load_extra_mcmc_get_chunkExtracts a vector of lines of data or output (a chunk) from...
load_extra_mcmc_get_parameter_chunkExtracts a vector of lines of data or output (a chunk) from...
load_extra_mcmc_init_nageLoad the inital numbers-at-age as defined in...
load_extra_mcmc_mLoad the natural mortality outputs from the extra MCMC output
load_extra_mcmc_recr_cohortsLoad the recruitment outputs from the extra MCMC output for...
load_extra_mcmc_repfilesLoad all SS3 report files from the directory provided and...
load_forecastsFetch the output from previously-run forecasting using...
load_mcmc_valsLoad some values from the MCMC output and store in a list
load_parameter_priorsLoad values (priors) from the 'parameters' data frame in the...
load_ss_filesLoad all the SS files for output and input, and return the...
main_alphaThe transparency to use by default for all fills in the plots...
main_fillThe color to use by default for all fills in the plots in the...
make_major_tick_labelsCreate a vector of x-axis tick labels by only populating the...
maturity_estimates_dfA data frame containing information on the maturity estimates...
maturity_samples_dfA data frame containing information on ovary sampling
mcmc_pathDirectory name for the mcmc output for models
minor_tick_lengthThe length of the minor tick marks in plots in cm
model_output_log_fnA character string containing the file name for the model...
model_setupLoad models and set up lists and classes for the base model,...
modify_starter_mcmc_typeChange the MCMC setting in an SS starter file so the extra...
mutselLink together 'dplyr::mutate()' and 'dplyr::select()'
nuisance_posteriors_fnA character string containing the file name for the nuisance...
number_to_wordChange a number into an English word
object_placement_fnName of file containing the object placement settings for...
obj_sizesReturn a data frame of the names and sizes of the objects in...
ordered_decision_table_pathsAn ordered vector of the paths used in the decision table for...
out_csv_pathDirectory name for outputting the CSV versions of at-age...
output_permissionsThe Linux file permissions value to use for fs::file_chmod()
ovary_samples_dfA data frame containing information on ovary sampling
pacea_saveSave some results as '.rds' files to then be imported into...
pad_numPad the beginning of numbers in a vector with zeroes so they...
pad_weight_at_ageFill in necessary years of weight-at-age file
par_fnA character string containing the file name for the SS3 par...
plot_age_comp_bubblesMake an age composition bubble plot
plot_age_comp_bubbles_dataCreate a multi-panel plot of age proportion bubble plots, one...
plot_age_comp_comparison_bubblesCreate a plot of age proportions as bubbles with fishery and...
plot_age_comp_fitCreate a set of barplots by year with the bars being observed...
plot_assessment_history_biomassTitle
plot_assessment_history_dispCreate Interquartile range or quartile coefficient of...
plot_assessment_timelineCreate a plot showing the relative numbers of days we have...
plot_autocorCreate an autocorrelation plot for a particular parameter
plot_biomassPlot biomass from MCMC output for one or more models....
plot_biomass_fished_unfishedPlot the fished biomass vs. the unfished biomass for a model
plot_bubblesMake a bubble plot from the given data
plot_catchability_densityPlot the density histogram for the posteriors for...
plot_catch_by_monthCreate a plot of cumulative catches, with one panel for each...
plot_catchesPlot catch data as a stacked barplot
plot_colorColors for the Hake Assessment
plot_comparisonCreate an n-panel plot of the biomass, relative biomass, or...
plot_cumulative_catch_cohortsCreates a plot showing the cumulative catches for certain...
plot_data_summaryCreate a plot with three panels showing a summary of the data...
plot_densityCreate a density plot for a particular parameter
plot_depthCreate a boxplot of depths for a given data frame
plot_depth_2_panelCreate a 2-panel plot with fishing depth on the left and...
plot_depth_4_panelCreate a 4-panel plot with fishing depth on the left and...
plot_during_loadingCreate plots during the loading phase, and return a list of...
plot_fecundityCreate a aplot of fecundity-at-age and mean-weight-at-age
plot_fore_age_compsCreate a two-panel plot showing the forecasted age...
plot_heatmap_sample_size_weight_at_ageCreate a weight-at-age heatmap including extrapolated years
plot_heatmap_weight_at_ageCreate a weight-at-age heatmap including extrapolated years
plot_historical_probsPlots to compare historical and current probabilities
plot_historical_probs_retroMake individual plots (or one overlaid) of historical...
plot_intensity_illustrationCreate a plot illustrating the fishing intensity as a...
plot_management_catch_vs_tacMake a time series plot of the management-chosen TAC,...
plot_management_catch_vs_tac_1_to_1Plot the TAC vs realized catch on a 1-to-1 plot
plot_mapCreate a map of a part of the west coast of North America,...
plot_maturity_ogivesCreate a plot containing the maturity ogives by year on a...
plot_mcmc_diagnosticsPlot MCMC diagnostics
plot_mcmc_diagnostics_all_paramsCreates the plot showing the 4 MCMC diagnostics for all...
plot_mcmc_histogramPlot a histogram for a given column in a data frame
plot_overview_mapCreate a map of the west coast of North America showing...
plot_pairsCreate a pairs plot showing correlations among key parameters...
plot_param_densityCreate a plot showing the density of the posterior for the...
plot_pearson_bubblesMake a bubble plot from the given data
plot_phaseCreate plot of the relative fishing intensity in year t-1...
plot_priors_vs_postsMake a grid of posterior plots with priors and initial values
plot_retro_recruitsMake squid plot of retrospectives of recruitment deviations.
plot_retro_yrsThe years previous to the end of the time series to include...
plot_running_quantsCreate a plot with running quantiles across the posterior for...
plot_selex_mountainsCreate a plot of median selectivity as a set of overlapping...
plot_selex_posteriorsPlot the selectivity parameter estimates from all posteriors...
plot_selex_uncertaintyCreate a plot of time-varying selectivity panels
plot_spatial_cpueCreate a map of the west coast of North America showing...
plot_spr_illustrationCreate a three-panel plot illustrating how the SPR is...
plot_squidMake the retrospective recruitment deviations plot (squid...
plot_stock_recruitmentCreate a plot of the stock-recruitment relationship with...
plot_survey_biomassCreate a plot of survey biomass as points with error bars
plot_survey_fit_mcmcCreates a plot of fits to survey biomass including individual...
plot_traceCreate a trace plot for a particular parameter
plot_weight_at_ageCreate a plot of weight-at-age lines by age and year
plot_weights_lengthsPlot some years of weight of length histograms
ports_dfA data frame containing information about the ports used in...
post_processPost-process the TEX file output by Bookdown
post_process_add_alt_textAdd alternative text to figures in the document via the...
post_process_add_appendix_counter_resetsAdd appendix counter rests LaTeX code for equations, figures,...
post_process_add_countersAdd LaTeX counter code so that the Executive summary has...
post_process_add_headers_footersAdd left and right footer text to the pages
post_process_add_horiz_lines_decision_tableAdds two horizontal lines to the decision tables
post_process_add_picture_to_title_pageInsert an image on the title page
post_process_add_start_appendices_codeAdd start appendices LaTeX code
post_process_add_vert_space_after_headerAdd LaTeX vertical space code after the Executive Summary...
post_process_beamerPost-process the TEX file output by Bookdown for beamer...
post_process_beamer_add_extra_headers_etcAdd extra headers needed for tables, colors in tables,...
post_process_beamer_insert_disclaimerInsert a disclaimer notice at the bottom of the title page of...
post_process_beamer_insert_title_page_logosInsert the NOAA and DFO logos and a hake picture on the title...
post_process_beamer_make_title_page_plainRemove theme shadow and navigation bar from the title page
post_process_convert_section_headersReplace chapter with section for all sections, and prepend a...
post_process_error_checkCheck the input LaTex for errors or omissions before post...
post_process_extract_chunksExtract chunks of lines from a vector of lines
post_process_fix_landscape_issuesRemove landscape/portrait code between tables/figures which...
post_process_fix_tildesChange tildes (~) so that they will make it through the...
post_process_interlace_chunksInterlace chunks of code that have been extracted by...
post_process_landscape_figuresPost-process landscape figures in TEX code
post_process_landscape_tablesPost-process landscape tables in TEX code
post_process_longtablesPost-process LaTeX longtables in TEX code
post_process_modify_font_infoModify the font type and size in the LaTeX code
post_process_modify_link_colorsModify reference link colors in the document
post_process_move_table_captionsMove certain table captions, usually to left-justify. There...
post_process_object_placementModify the tex code 'x' by changing the table or figure label...
post_process_remove_title_page_numberRemoves the page number from the title page
post_process_repair_unnumbered_section_linksAdd phantomsection tag to sections that are unnumbered to...
post_process_set_latex_placement_optionsInject LaTeX float placement codes for figure and tables,...
post_process_table_of_contentsInsert the table of contents into TeX code
posts_fnA character string containing the file name for the SS3...
probsA vector of the probabilities to use for uncertainty...
probs_forecastA vector of the probabilities to use for uncertainty...
psv_fnA character string containing the file name for the SS3 psv...
rbeta_abThe Beta distribution
read_bookdown_fileRead a _bookdown.yml file into a reasonable format which is a...
recruit_dev_start_yrThe year in which the recruitment deviations start in the...
refpt_bo_linecolorThe color of the horizontal line representing B0
refpt_bo_linetypeThe default line type to use for the horizontal line...
refpt_bo_linewidthThe default line width to use for the horizontal line...
refpt_lrp_linecolorThe color of the horizontal line representing the limit...
refpt_lrp_linetypeThe default line type to use for the horizontal line...
refpt_lrp_linewidthThe default line width to use for the horizontal line...
refpt_usr_linecolorThe color of the horizontal line representing the upper stock...
refpt_usr_linetypeThe default line type to use for the horizontal line...
refpt_usr_linewidthThe default line width to use for the horizontal line...
regex_eml_recdevsRegular expression for the "early", "main", and "late"...
regex_extra_mcmc_compreportRegular expression for the CompReport files in the extra MCMC...
regex_extra_mcmc_reportRegular expression for the Report files in the extra MCMC...
regex_main_recdevsRegular expression for the "main" recruitment deviation...
regex_recdev_allRegular expression for the "early", "main", and "late"...
regex_recdev_earlyRegular expression for the "early initial" (Early_InitAge)...
remove_forecast_outputsRemove the 'outputs' list item from the 'catch_levels' lists...
renderRender the Hake assessment document PDF file
replace_dotted_pathsReplace dotted paths in the vector with their correct full...
report_fnA character string containing the file name for the SS3...
retropectives_pathDirectory name for storing the retrospectives.
retrospectives_prependName to be prepended to year for retrospective directory...
retrospective_yrsThe years previous to the end of the time series to strip off...
rich_colors_shortCreate rich colors as RGB strings
run_adnutsRun the adnuts MCMC for the model found in the directory...
run_adnuts_timedRun 'run_adnuts()' with a timer
run_catch_levels_copy_input_filesCopy the necessary files from a models' work directories to...
run_ct_levelsA wrapper to run the catch levels determination routines
run_ct_levels_default_hrRun the model, iteratively reducing the difference between...
run_ct_levels_spr_100Run the model iteratively zoning in on a catch value that...
run_ct_levels_stable_catchRun the model iteratively reducing the difference between the...
run_extra_forecastsRun extra forecasting for the model supplied
run_forecastsRun forecasting for a model in parallel when possible
run_retrospectivesRuns retrospectives for the given model and for the vector of...
sampling_history_dfA data frame containing information on amount of sampling...
save_nuts_fitsRead in NUTS run data files ('hake.Rdata' files), fix the...
set_ct_levelsReads in the forecast description data and creates the list...
set_dirsSet and return all model directories for the project
show_ss_outputA character string containing the name of the variable flag...
split_prior_infoExtract priors information from a string with a particular...
spr_100_pathDirectory name for storing the SPR 100 catch levels
sql_pathDirectory name for any SQL code files
ss_executableA character string containing the name of the SS3 executable...
ss_input_filesA vector of character strings containing the file names...
sso_pathDirectory name for the mcmc output when MCMC_output_detail in...
stable_catch_pathDirectory name for storing the stable catch catch levels
starter_fnA character string containing the file name for the SS3...
start_yrThe starting year for the model estimates
start_yr_age_compsThe starting year for the age composition data in the model
states_dfA data frame containing information about the states and...
stop_quietlyStop the program without issuing an error message
survey_end_yrThe last year for the acoustic survey in the model
survey_history_dfA data frame containing information about the history of all...
survey_start_yrThe starting year for the acoustic survey in the model
surv_yrsA vector of years in which the acoustic survey took place and...
system_Call 'shell()' or 'system()' depending on the Operating...
table_above_avg_cohorts_yrsCreate a table containing some years' estimated recruitment...
table_age_dataCreates a table containing single-fleet age proportions which...
table_assessment_changesTitle
table_at_ageMakes a table of the estimated -at-age values for 5 different...
table_biomassCreate a table of spawning biomass and relative spawning...
table_catchCreate a table of total catch
table_catch_by_fleetCreate a table containing the catch-at-age for one of the 3...
table_catch_tac_summaryCreate a table of US vs Canadian catch, TAC, and attainment...
table_ci_posteriorsMake a latex table of credible intervals with columns for...
table_cohortCreate a table of cohort biomass and natural mortality as...
table_decisionCreate the Executive Summary decision tables. 'rows_to_label'...
table_decision_originalCreate the Executive Summary decision tables. 'rows_to_label'...
table_fishing_intensityCreate a table of fishing intensity and exploitation fraction...
table_fore_age_propsCreates a table showing the forecast age comp percentages by...
table_input_age_dataCreates a table containing the age data which are input into...
table_landings_tacCreate a summary table of landings and TACS
table_maturity_ogiveCreate a table containing the maturiy ogive data as input...
table_median_posteriorsMake a latex table of medians with columns for female...
table_ovary_samplesCreate a table containing the ovary sampling information
table_param_estReturns a 'kableExtra::kbl()' containing a comparison of...
table_param_est_last_year_hardcodedReturns a 'kableExtra::kbl()' containing a comparison of...
table_parameters_long_summaryTitle
table_recruitmentCreate a table of absolute recruitment and relative spawning...
table_reference_pointsCreates a table containing reference point estimates
table_riskCreates LaTeX code to make a probability of risk table with...
table_sampling_by_monthExtract the number of samples by fleet and month for a given...
table_sampling_historyCreates a table of the sampling history for hake
table_survey_by_countryCreate a table of values of the age 2+ survey biomass...
table_survey_historyCreate a table of the acoustic survey history
table_yearly_model_compareCreate a table comparing this year's biomass estimate and...
top_cohCreate text describing the top 'num_cohorts' cohorts by year...
ts_linegapThe gap between the lines connecting the median points in the...
ts_linewidthThe line width to use for the line connecting the median...
ts_pointshapeThe point shape to use for the medians in the time series...
ts_pointsizeThe point size to use for the medians in the time series...
ts_pointstrokeThe point stroke (boldness) to use for the points...
ts_ribbon_alphaThe transparency to use by default to fill time series CI...
ts_ribbon_linetypeThe line type for the edges of the CI ribbon for time series...
ts_single_model_linecolorThe line color to use for the line connecting the median...
ts_single_model_linetypeThe line type to use for the line connecting the median...
ts_single_model_linewidthThe line width to use for the line connecting the median...
ts_single_model_pointcolorThe point color to use for the median points in the time...
ts_single_model_pointshapeThe point shape to use for the points representing the median...
ts_single_model_pointsizeThe point size to use for the points representing the median...
ts_single_model_pointstrokeThe point stroke (boldness) to use for the points...
ts_single_model_ribbon_fillThe color to use to fill time series CI ribbons for plots...
ts_single_model_ribbon_linetypeThe line type to use for the borders on the CI ribbons for...
unfished_eq_yrThe year in which unfished equilibrium is set
update_ss3_ageing_errorInsert ageing error matrix if needed
update_ss3_catchUpdate the catches in a Stock Synthesis file
update_ss3_maturityUpdate maturity in an SS3 weight-at-age matrix
us_atsea_bottom_depth_dfA data frame containing information about the depths of the...
us_atsea_fishing_depth_dfA data frame containing information about the depths of the...
us_cp_age_dfA data frame containing information about the proportions of...
us_cp_age_props_fnThe filename for the Catcher-processor fleet age proportions...
us_cp_catch_by_month_dfA data frame containing catch information on U.S....
us_cp_prop_tacThe proportion of the U.S. TAC that the Catcher-processor...
us_extract_sampling_by_monthExtract the number of ages, lengths, and weights month for...
us_ms_age_dfA data frame containing information about the proportions of...
us_ms_age_props_fnThe filename for the U.S. Mothership fleet age proportions by...
us_ms_catch_by_month_dfA data frame containing catch information on U.S. ti vessels...
us_ms_prop_tacThe proportion of the U.S. TAC that the Mothership sector...
us_research_catch_by_month_dfA data frame containing catch information on U.S. research...
us_sb_age_props_fnThe filename for the U.S. Shore-based fleet age proportions...
us_ss_age_dfA data frame containing information about the proportions of...
us_ss_catch_by_month_dfA data frame containing catch information on U.S. shore-based...
us_ss_prop_tacThe proportion of the U.S. TAC that the Shore-based sector...
us_ti_ct_by_month_dfA data frame containing catch information on U.S. tribal...
utils_update_catch_sumsUpdates the most recent catch time values stored in...
vec2dfCreate a one-row data frame from a vector of values
weight_age_sample_sizes_dfA data frame containing information on weight-at-age
weight_at_age_fnA character string containing the file name for the SS3...
yaml_check_margin_formatCheck the format of the margin command entered into the YAML...
pacific-hake/hake-assessment documentation built on June 10, 2024, 2:22 p.m.