API for pacific-hake/hake-assessment
Stock Assessment for Pacific Hake

Global functions
.onLoad Source code
.onUnload Source code
add_extra_ribbon_data Man page Source code
add_major_ticks Man page Source code
add_newlines Man page Source code
add_utm_columns Man page Source code
age_bubble_cohorts Man page
age_diag_linecolor Man page
age_diag_linetype Man page
age_diag_linewidth Man page
age_fillcolor Man page
alt_text_inject_tags Man page Source code
as_ts_mcmc Man page Source code
assess_changes_df Man page
assess_history_df Man page
assess_history_probs_df Man page
axis_label_color Man page
axis_tick_font_size Man page
axis_title_font_size Man page
beta_get_shape_params Man page Source code
bind_cols_quiet Man page Source code
calc_ageerror Man page Source code
calc_fishery_ages Man page Source code
calc_historical_probs Man page Source code
calc_lw_params Man page Source code
calc_mcmc Man page Source code
calc_mcmc_param_stats Man page Source code
calc_quantiles Man page Source code
calc_quantiles_by_group Man page Source code
calc_refpt_quants Man page Source code
calc_retro_stats Man page Source code
calc_risk Man page Source code
calc_sum_rec_devs Man page Source code
calc_yoob Man page Source code
can_catch_by_year_fn Man page
can_ft_age_df Man page
can_ft_age_props_fn Man page
can_ft_bottom_depth_df Man page
can_ft_catch_by_month_df Man page
can_ft_catch_by_month_fn Man page
can_ft_gear_depth_df Man page
can_ft_num_fish Man page
can_jv_age_props_fn Man page
can_jv_catch_by_month_df Man page
can_jv_catch_by_month_fn Man page
can_jv_num_fish Man page
can_raw_ft_age_counts_fn Man page
can_raw_jv_age_counts_fn Man page
can_raw_ss_age_counts_fn Man page
can_sample_data_rds_fn Man page
can_ss_age_df Man page
can_ss_age_props_fn Man page
can_ss_bottom_depth_df Man page
can_ss_catch_by_month_df Man page
can_ss_catch_by_month_fn Man page
can_ss_gear_depth_df Man page
can_ss_num_fish Man page
can_waa_fn Man page
canada_create_age_proportions_csv Man page Source code
canada_create_commercial_waa Man page Source code
canada_create_fleet_month_catch_csv_files Man page Source code
canada_create_fleet_year_catch_csv_files Man page Source code
canada_depth_sql_fn Man page
canada_extract_depth_data_from_db Man page Source code
canada_extract_fleet_catch Man page Source code
canada_extract_samples_from_db Man page Source code
canada_extract_sampling_by_month Man page Source code
canada_get_fleet_samples Man page Source code
canada_load_catch_data Man page Source code
canada_load_sample_data Man page Source code
canada_sql_inject_fishery_filters Man page Source code
caption_adjustments_fn Man page
catch_targets_biomass_fn Man page
catch_targets_df Man page
check_catch_levels Man page Source code
check_forecasts Man page Source code
clean Man page Source code
clean_all Man page Source code
cohort_catch Man page Source code
combine_historical_probs Man page Source code
comp_report_fn Man page
compute_hexagon_xy Man page Source code
control_fn Man page
convert_ctl_file_param_dfs Man page Source code
covar_fn Man page
create_data_hake Man page Source code
create_depth_by_year_csv_files Man page Source code
create_fontsize_str Man page Source code
create_group_df_biomass Man page Source code
create_group_df_index Man page Source code
create_group_df_recr Man page Source code
create_rds_attach_forecasts Man page Source code
create_rds_attach_retrospectives Man page Source code
create_rds_file Man page Source code
create_rds_files_retro Man page Source code
create_sens_dirs Man page Source code
create_version_dirs Man page Source code
ct Man page
ct_levels_catch_tol Man page
ct_levels_max_iter Man page
ct_levels_path Man page
ct_levels_spr_tol Man page
curr_time_date Man page Source code
data_fn Man page
data_new_ssnew_fn Man page
data_ssnew_fn Man page
data_tables_path Man page
dbeta_ab Man page Source code
default_hr_path Man page
delete_dirs Man page Source code
delete_rds_files Man page Source code
derposts_fn Man page
dirclip Man page Source code
doc_path Man page
draw_arrows_yoob Man page Source code
enact_privacy_rule Man page Source code
extract_alt_text Man page Source code
extract_inline_rcode Man page Source code
extract_inside_catch Man page Source code
extract_label_from_figure_filename Man page Source code
extract_mcmc_quant Man page Source code
extract_rep_table Man page Source code
extract_sigma_r Man page Source code
extract_survey_index_fits Man page Source code
f Man page Source code
firstup Man page Source code
fit_lw Man page Source code
fix_posteriors Man page Source code
fix_title_case_for_csl Man page Source code
forecast_descriptions_fn Man page
forecast_fn Man page
forecasts_path Man page
forecasts_prepend Man page
further_tac_details_fn Man page
further_tac_df Man page
get_age_comp_limits Man page Source code
get_age_prop Man page Source code
get_age_proportions_by_fleet Man page Source code
get_assess_yr Man page Source code
get_col_name_from_key_title Man page Source code
get_crs Man page Source code
get_doc_type Man page Source code
get_key_nuisance_posts Man page Source code
get_obj_sizes Man page Source code
get_os Man page Source code
get_param_est_comparison_df Man page Source code
get_post_cols Man page Source code
get_posterior_data Man page Source code
get_prior_data Man page Source code
get_prior_string Man page Source code
get_rec_ci Man page Source code
get_ss3_exe_name Man page Source code
get_year_range Man page
goback Man page Source code
gotest Man page Source code
gotest_beamer_get_src_dest_filenames Man page Source code
gotest_doc_get_src_dest_filenames Man page Source code
group_test_models Man page
hake Man page
hake_beamer Man page Source code
hake_pdf Man page Source code
hake_theme Man page Source code
heatmap_add_extrap_yrs_wa Man page Source code
heatmap_calc_function Man page Source code
heatmap_extract_sample_size Man page Source code
heatmap_get_wa_ggplot_vals Man page Source code
heatmap_set_colors Man page Source code
hex_coords Man page
insert_row Man page Source code
key_posteriors Man page
key_posteriors_fn Man page
key_posteriors_titles Man page
kriging_pars_df Man page
landings_tac_fn Man page
large_cohorts Man page
latex_amp Man page Source code
latex_bold Man page Source code
latex_cline Man page Source code
latex_italics Man page Source code
latex_mcol Man page Source code
latex_size_str Man page Source code
latex_subscr Man page Source code
latex_under Man page Source code
linebreaker Man page Source code
load_all_models_in_subdir Man page
load_can_age_data Man page Source code
load_ct_levels Man page Source code
load_extra_mcmc Man page Source code
load_extra_mcmc_age_comps Man page Source code
load_extra_mcmc_atage Man page Source code
load_extra_mcmc_biomass Man page Source code
load_extra_mcmc_catage_biomass Man page Source code
load_extra_mcmc_get_chunk Man page Source code
load_extra_mcmc_get_parameter_chunk Man page Source code
load_extra_mcmc_init_nage Man page Source code
load_extra_mcmc_m Man page Source code
load_extra_mcmc_naa Source code
load_extra_mcmc_recr_cohorts Man page Source code
load_extra_mcmc_recr_devs Source code
load_extra_mcmc_repfiles Man page Source code
load_extra_mcmc_sel Man page Source code
load_extra_mcmc_selwt Man page Source code
load_forecasts Man page Source code
load_mcmc_vals Man page Source code
load_parameter_priors Man page Source code
load_ss_files Man page Source code
main_alpha Man page
main_fill Man page
make_major_tick_labels Man page Source code
maturity_estimates_df Man page
maturity_samples_df Man page
mcmc_path Man page
minor_tick_length Man page
model_output_log_fn Man page
model_setup Man page Source code
modify_starter_mcmc_type Man page Source code
mutsel Man page
nuisance_posteriors_fn Man page
number_to_word Man page Source code
obj_sizes Man page Source code
object_placement_fn Man page
ordered_decision_table_paths Man page
out_csv_path Man page
output_permissions Man page
ovary_samples_df Man page
pacea_save Man page Source code
pad_num Man page Source code
pad_weight_at_age Man page Source code
par_fn Man page
plot_age_comp_bubbles Man page Source code
plot_age_comp_bubbles_data Man page Source code
plot_age_comp_comparison_bubbles Man page Source code
plot_age_comp_fit Man page Source code
plot_assessment_history_biomass Man page Source code
plot_assessment_history_disp Man page Source code
plot_assessment_timeline Man page Source code
plot_autocor Man page Source code
plot_biomass Man page Source code
plot_biomass_fished_unfished Man page
plot_bubbles Man page Source code
plot_catch_by_month Man page Source code
plot_catchability_density Man page Source code
plot_catches Man page Source code
plot_cohort_catch Man page Source code
plot_color Man page Source code
plot_comparison Man page
plot_cumulative_catch_cohorts Man page Source code
plot_data_summary Man page Source code
plot_density Man page Source code
plot_depl_fore_comparison Man page Source code
plot_depth Man page Source code
plot_depth_2_panel Man page Source code
plot_depth_4_panel Man page Source code
plot_during_loading Man page Source code
plot_exploitation_fraction Man page Source code
plot_fecundity Man page Source code
plot_fishing_intensity Man page Source code
plot_fore_age_comps Man page Source code
plot_fore_compare Man page Source code
plot_heatmap_sample_size_weight_at_age Man page Source code
plot_heatmap_weight_at_age Man page Source code
plot_historical_probs Man page Source code
plot_historical_probs_retro Man page Source code
plot_intensity_illustration Man page Source code
plot_management_catch_vs_tac Man page Source code
plot_management_catch_vs_tac_1_to_1 Man page Source code
plot_map Man page Source code
plot_maturity_ogives Man page Source code
plot_mcmc_diagnostics Man page Source code
plot_mcmc_diagnostics_all_params Man page Source code
plot_mcmc_histogram Man page Source code
plot_overview_map Man page Source code
plot_pairs Man page Source code
plot_param_density Man page Source code
plot_pearson_bubbles Man page Source code
plot_phase Man page Source code
plot_priors_vs_posts Man page Source code
plot_recdevs Man page Source code
plot_recruitment Man page Source code
plot_rel_biomass Man page Source code
plot_rel_recruitment Man page Source code
plot_retro_recruits Man page Source code
plot_retro_yrs Man page
plot_running_quants Man page Source code
plot_selex_mountains Man page Source code
plot_selex_posteriors Man page Source code
plot_selex_uncertainty Man page Source code
plot_spatial_cpue Man page Source code
plot_spr_illustration Man page Source code
plot_squid Man page Source code
plot_stock_recruitment Man page
plot_survey_biomass Man page Source code
plot_survey_fit_mcmc Man page Source code
plot_survey_index_fits Man page Source code
plot_trace Man page Source code
plot_weight_at_age Man page Source code
plot_weights_lengths Man page Source code
ports_df Man page
post_process Man page Source code
post_process_add_alt_text Man page Source code
post_process_add_appendix_counter_resets Man page Source code
post_process_add_counters Man page Source code
post_process_add_headers_footers Man page Source code
post_process_add_horiz_lines_decision_table Man page Source code
post_process_add_picture_to_title_page Man page Source code
post_process_add_start_appendices_code Man page Source code
post_process_add_vert_space_after_header Man page Source code
post_process_add_xcolor_package Source code
post_process_beamer Man page Source code
post_process_beamer_add_extra_headers_etc Man page Source code
post_process_beamer_insert_disclaimer Man page Source code
post_process_beamer_insert_title_page_logos Man page Source code
post_process_beamer_make_title_page_plain Man page Source code
post_process_convert_section_headers Man page Source code
post_process_error_check Man page Source code
post_process_extract_chunks Man page Source code
post_process_fix_landscape_issues Man page Source code
post_process_fix_tildes Man page Source code
post_process_interlace_chunks Man page Source code
post_process_landscape_figures Man page Source code
post_process_landscape_tables Man page Source code
post_process_longtables Man page Source code
post_process_modify_font_info Man page Source code
post_process_modify_link_colors Man page Source code
post_process_move_table_captions Man page Source code
post_process_object_placement Man page Source code
post_process_remove_title_page_number Man page Source code
post_process_repair_unnumbered_section_links Man page Source code
post_process_set_latex_placement_options Man page Source code
post_process_table_of_contents Man page Source code
posts_fn Man page
probs Man page
probs_forecast Man page
psv_fn Man page
rbeta_ab Man page Source code
read_bookdown_file Man page Source code
recruit_dev_start_yr Man page
refpt_bo_linecolor Man page
refpt_bo_linetype Man page
refpt_bo_linewidth Man page
refpt_lrp_linecolor Man page
refpt_lrp_linetype Man page
refpt_lrp_linewidth Man page
refpt_usr_linecolor Man page
refpt_usr_linetype Man page
refpt_usr_linewidth Man page
regex_eml_recdevs Man page
regex_extra_mcmc_compreport Man page
regex_extra_mcmc_report Man page
regex_main_recdevs Man page
regex_recdev_all Man page
regex_recdev_early Man page
remove_forecast_outputs Man page Source code
render Man page Source code
replace_dotted_paths Man page Source code
report_fn Man page
retropectives_path Man page
retrospective_yrs Man page
retrospectives_prepend Man page
rich_colors_short Man page Source code
run_adnuts Man page Source code
run_adnuts_timed Man page Source code
run_catch_levels_copy_input_files Man page Source code
run_ct_levels Man page Source code
run_ct_levels_default_hr Man page Source code
run_ct_levels_spr_100 Man page Source code
run_ct_levels_stable_catch Man page Source code
run_extra_forecasts Man page Source code
run_forecasts Man page Source code
run_retrospectives Man page Source code
sampling_history_df Man page
sanitize.text.function Source code
save_nuts_fits Man page Source code
set_ct_levels Man page Source code
set_dirs Man page Source code
show_ss_output Man page
split_prior_info Man page Source code
spr_100_path Man page
sql_path Man page
ss_executable Man page
ss_input_files Man page
sso_path Man page
stable_catch_path Man page
start_yr Man page
start_yr_age_comps Man page
starter_fn Man page
states_df Man page
stop_quietly Man page Source code
surv_yrs Man page
survey_end_yr Man page
survey_history_df Man page
survey_start_yr Man page
system_ Man page Source code
table_above_avg_cohorts_yrs Man page Source code
table_age_data Man page Source code
table_assessment_changes Man page Source code
table_at_age Man page Source code
table_biomass Man page Source code
table_catch Man page Source code
table_catch_by_fleet Man page Source code
table_catch_tac_summary Man page Source code
table_ci_posteriors Man page Source code
table_cohort Man page Source code
table_decision Man page
table_decision_original Man page Source code
table_fishing_intensity Man page Source code
table_fore_age_props Man page Source code
table_input_age_data Man page Source code
table_landings_tac Man page Source code
table_maturity_ogive Man page Source code
table_median_posteriors Man page Source code
table_ovary_samples Man page Source code
table_param_est Man page Source code
table_param_est_bounds Man page Source code
table_param_est_last_year_hardcoded Man page Source code
table_parameters_long_summary Man page Source code
table_recruitment Man page Source code
table_reference_points Man page Source code
table_risk Man page Source code
table_sampling_by_month Man page Source code
table_sampling_history Man page Source code
table_survey_by_country Man page Source code
table_survey_history Man page Source code
table_yearly_model_compare Man page Source code
test_extract_inline_rcode Source code
top_coh Man page Source code
ts_linegap Man page
ts_linewidth Man page
ts_pointshape Man page
ts_pointsize Man page
ts_pointstroke Man page
ts_ribbon_alpha Man page
ts_ribbon_linetype Man page
ts_single_model_linecolor Man page
ts_single_model_linetype Man page
ts_single_model_linewidth Man page
ts_single_model_pointcolor Man page
ts_single_model_pointshape Man page
ts_single_model_pointsize Man page
ts_single_model_pointstroke Man page
ts_single_model_ribbon_fill Man page
ts_single_model_ribbon_linetype Man page
unfished_eq_yr Man page
update_ss3_ageing_error Man page Source code
update_ss3_catch Man page Source code
update_ss3_maturity Man page Source code
us_atsea_bottom_depth_df Man page
us_atsea_fishing_depth_df Man page
us_cp_age_df Man page
us_cp_age_props_fn Man page
us_cp_catch_by_month_df Man page
us_cp_prop_tac Man page
us_extract_sampling_by_month Man page Source code
us_ms_age_df Man page
us_ms_age_props_fn Man page
us_ms_catch_by_month_df Man page
us_ms_prop_tac Man page
us_research_catch_by_month_df Man page
us_sb_age_props_fn Man page
us_ss_age_df Man page
us_ss_catch_by_month_df Man page
us_ss_prop_tac Man page
us_ti_ct_by_month_df Man page
utils_update_catch_sums Man page Source code
vec2df Man page Source code
weight_age_sample_sizes_df Man page
weight_at_age_fn Man page
yaml_check_margin_format Man page Source code
pacific-hake/hake-assessment documentation built on June 10, 2024, 2:22 p.m.