diff --git a/.gitignore b/.gitignore index 9c4a923..15c066d 100644 --- a/.gitignore +++ b/.gitignore @@ -3,3 +3,4 @@ .RData .Ruserdata petrale_convert_output.csv +captions_alt_text.csv diff --git a/R/write_captions.R b/R/write_captions.R index 2d8dd64..61e55e1 100644 --- a/R/write_captions.R +++ b/R/write_captions.R @@ -246,9 +246,18 @@ write_captions <- function(dat, # converted model output object # TABLES----- + ## catch + # catch_fleet <- # fleet + + ## landings + # landings_tbl_units <- # landings units; remove if units already in table + + ## discards + # discards_tbl_units <- # discards units ## catchability - # + # catchability_fleet <- # fleet + # add in more quantities here, and update the quantities above diff --git a/inst/resources/captions_alttext.csv b/inst/resources/captions_alttext.csv index 0e08171..997e701 100644 --- a/inst/resources/captions_alttext.csv +++ b/inst/resources/captions_alttext.csv @@ -15,7 +15,6 @@ CPUE_indices,figure,Catch per unit effort (CPUE) over time for fleet or survey. NAA,figure,Model estimate of population numbers at age over time. The relative size of each bubble for a given year and age indicates the relative abundance in that category compared with others. ,"Bubble plot showing relative age proportions over time. The x axis, showing the year, spans from bubble_start_year to bubble_end_year, and the y axis, showing age in bubble_age_units, spans from bubble_age_min to bubble_age_max." mod_fit_catch,figure,Observed catch from the data input file (points) and model estimated catch (line) over time for fleet_or_survey_name. ,"Point and line graph showing observed catch from the data input file as points and model estimated catch as a line over time for fleet_or_survey_name. The x axis, showing years, spans from mod_fit_catch_start_year to mod_fit_catch_end_year and the y axis, showing catch in mod_fit_catch_units, spans from mod_fit_catch_min to mod_fit_catch_max." mod_fit_abun,figure,Assessment model fits to input catch per unit of effort index values over time calculated from fleet_or_survey_name.,"Point and line graph showing the assessment model fit, displayed as a line, to input catch per unit effort index values, displayed as points over time, for fleet_or_survey_name. The x axis, showing years, spans from mod_fit_abun_start_year to mod_fit_abun_end_year, and the y axis, showing catch per unit effort in cpue_units, spans from cpue_min to cpue_max." -catchability,figure,catchability caption here,catchability alt text here mod_fit_discards,figure,Observed discards (points) and model-estimated discards (line).,"Point and line graph showing the assessment model fit to observed discards. Observed discards are represented as points while the model fitted estimates are represented as a line over time for fleet_or_survey_name. The x axis, showing the year, spans from mod_fit_discards_start_year to mod_fit_discards_end_year, and the y axis, showing discards in mod_fit_discards_units, spans from mod_fit_discards_min to mod_fit_discards_max." selectivity,figure,Length-based selectivity for each fleet and survey estimated by the assessment model.,"Line graph showing length-based selectivity for fleet_or_survey_name from selectivity_start_year to selectivity_end_year. The x axis, showing length in selectivity_length_units, spans from selectivity_length_min to selectivity_length_max, and the y axis, showing the proportion of the stock that the gear selects for, spans from 0–1." est_stock_recruitment,figure,Stock recruitment relationship estimated by the assessment model. ,"Point and line graph showing the relationship between spawning stock biomass and newly recruited est_stock_recruitment_age_min fish as estimated by the assessment model. Points represent model estimates of recruitment each year as a function of spawning stock biomass, after adjusted by annual recruitment deviations. The line represents the best fit through the points for the spawning stock relationship selected for use in the assessment model. The x axis, showing spawning stock biomass in est_stock_recruitment_ssb_units, spans from est_stock_recruitment_ssb_min to est_stock_recruitment_ssb_max, while the y axis, showing recruitment in est_stock_recruitment_units, spans from est_stock_recruitment_min to est_stock_recruitment_max." @@ -27,6 +26,21 @@ spr,figure,Model-estimated spawning potential ratio (SPR) (SSB~current~/SSB~targ pop_naa_baa,figure,Model-estimated population numbers at age and population biomass at age over time. The relative size of each bubble for a given year and age indicates the relative abundance or biomass in that category compared with others. ,"Bubble plot showing model-estimated population numbers at age and population biomass at age. The x axis, showing the year, spans from pop_naa_baa_start_year to pop_naa_baa_end_year, and the y axis, showing numbers of fish, spans from pop_naa_baa_fish_min to pop_naa_baa_fish_max." proj_catch,figure,Forecasted catch in proj_catch_units over future years for different fishing mortality scenarios as indicated in the legend.,"Time series line graph showing forecasted catch over future years for different fishing mortality scenarios. The x axis, showing the year, spans from proj_catch_start_year to proj_catch_end_year, and the y axis, showing catch in proj_catch_units, spans from proj_catch_min to proj_catch_max." proj_biomass,figure,Forecasted biomass in proj_biomass_units over future years for different fishing mortality scenarios as indicated in the legend. The horizontal dashed line represents the biomass limit reference point. ,"Time series line graph showing forecasted biomass over future years for different fishing mortality scenarios. The horizontal dashed line represents the biomass limit reference point. The x axis, showing the year, spans from proj_biomass_start_year to proj_biomass_end_year, and the y axis, showing biomass in proj_biomass_units, spans from proj_biomass_min to proj_biomass_max." -recruitment,table,recruitment table caption here, -spawning_biomass,table,spawning biomass table caption here, -indices,table,indices table caption here, +report_version_model_changes,table,Document version history briefly describing when major changes or updates are made to each version of the report. , +projection_ts,table,Forecasted catch and biomass over future years for different fishing mortality scenarios. , +catch,table,Observed (points) and model estimated (line) catch over time for fleet catch_fleet., +life_history_params,table,Life history parameters used in the stock assessment model. The last column of the table indicates whether the parameters were estimated by the model or fixed. , +landings,table,Landed catch by fleet and year in landings_tbl_units. , +discards,table,Discarded catch by fleet and year in discards_tbl_units. , +age_length_key,table,Age-length key: the proportion of fish for each age that belong to a particular length group. , +indices_abundance,table,Calculated indices of abundance and their corresponding CVs for the fleets and surveys identified in the column headers. , +model_runs,table,"The base configuration and alternative sensitivity analysis configurations of the stock assessment model, in which parameters and/or data input streams are changed from one configuration to another. ", +derived_quantities,table,Derived quantities calculated by the base configuration of the stock assessment model. , +est_params,table,Parameters used in the base stock assessment model and whether the parameter was estimated by the model or fixed (i.e. not allowed to be estimated or changed by the model). CVs for estimated models are provided., +F_per_fleet_per_year,table,Partial fishing mortality estimates for each fleet in the assessment model. , +B_div_N,table,"Historical biomass, abundance, and catch time series estimated by the base configuration of the stock assessment model. ", +naa,table,Historical population abundance (numbers) estimated by the base model for each age group., +catchability,table,Catchability over time for fleet catchability_fleet. , +sensitivity_runs,table,"Forecasted catch, biomass, spawning biomass, recruitment, fishing mortality, and stock status as projected from the base model configuration. ", +,,, +,,,