From dc17837f0497d4ed1a773126e0b4e0cc9ad74c10 Mon Sep 17 00:00:00 2001 From: sbreitbart-NOAA Date: Wed, 18 Dec 2024 16:00:42 -0500 Subject: [PATCH] Changed underscores to periods in key quantities to avoid issues with underscores being recognized as special characters in latex script --- R/write_captions.R | 659 +++++++++--------- inst/resources/captions_alt_text_template.csv | 90 +-- 2 files changed, 375 insertions(+), 374 deletions(-) diff --git a/R/write_captions.R b/R/write_captions.R index 985ada3..7448f88 100644 --- a/R/write_captions.R +++ b/R/write_captions.R @@ -27,28 +27,27 @@ write_captions <- function(dat, # converted model output object # extract key quantities # REMINDERS: # -the variable names must exactly match those in the captions/alt text csv. - # -quantities should be rounded to the nearest whole number. # FIGURES----- ## kobe plot - # B_BMSY_min <- # minimum value of B/B(MSY) - # B_BMSY_max <- # maximum value of B/B(MSY) - # F_FMSY_min <- # minimum value of F/F(MSY) - # F_FMSY_max <- # maximum value of F/F(MSY) - # B_BMSY_end_yr <- # value of B/B(MSY) at the end year - # F_FMSY_end_yr <- # value of F/F(MSY) at the end year - # overfished_status_is_isnot <- # object that should be "is" or "is not" and answers the question, "the stock overfishing status ___ overfished" - # overfishing_status_is_isnot <- # object that should be "is" or "is not" and answers the question, "the stock ___ experiencing overfishing" - # kobe_start_year <- # start year of kobe plot - # kobe_end_year <- # end year of kobe plot + # B.BMSY.min <- # minimum value of B/B(MSY) + # B.BMSY.max <- # maximum value of B/B(MSY) + # F.FMSY.min <- # minimum value of F/F(MSY) + # F.FMSY.max <- # maximum value of F/F(MSY) + # B.BMSY.end.yr <- # value of B/B(MSY) at the end year + # F.FMSY.end.yr <- # value of F/F(MSY) at the end year + # overfished.status.is.isnot <- # object that should be "is" or "is not" and answers the question, "the stock overfishing status ... overfished" + # overfishing.status.is.isnot <- # object that should be "is" or "is not" and answers the question, "the stock ... experiencing overfishing" + # kobe.start.year <- # start year of kobe plot + # kobe.end.year <- # end year of kobe plot ## Biomass plot - # B_ref_pt <- # biomass reference point- SHARED with kobe plot, above - # B_ref_pt_units <- # biomass reference point unit + # B.ref.pt <- # biomass reference point- SHARED with kobe plot, above + # B.ref.pt.units <- # biomass reference point unit # start year of biomass plot - B_start_year <- dat |> + B.start.year <- dat |> dplyr::filter(label == "biomass", module_name == "TIME_SERIES" | module_name == "t.series", # SS3 and BAM target module names is.na(fleet), @@ -59,15 +58,15 @@ write_captions <- function(dat, # converted model output object as.numeric() # end year of biomass plot - # B_end_year <- # this will take some thought, since end_year is + # B.end.year <- # this will take some thought, since end_year is # either entered by the user or calculated in plot_biomass.R # units of B (plural) - # B_units <- # this will take some thought, since units is + # B.units <- # this will take some thought, since units is # entered by the user in plot_biomass.R # minimum B - B_min <- dat |> + B.min <- dat |> dplyr::filter(label == "biomass", module_name == "TIME_SERIES" | module_name == "t.series", # SS3 and BAM target module names is.na(fleet), @@ -79,7 +78,7 @@ write_captions <- function(dat, # converted model output object round(digits = 2) # maximum B - B_max <- dat |> + B.max <- dat |> dplyr::filter(label == "biomass", module_name == "TIME_SERIES" | module_name == "t.series", # SS3 and BAM target module names is.na(fleet), @@ -111,29 +110,29 @@ write_captions <- function(dat, # converted model output object ## relative B # relative B min - rel_B_min <- (B_min / Btarg) |> + rel.B.min <- (B.min / Btarg) |> round(digits = 2) # relative B max - rel_B_max <- (B_max / Btarg) |> + rel.B.max <- (B.max / Btarg) |> round(digits = 2) ## mortality (F) plot - # F_ref_pt <- # F reference point - # F_ref_pt_units <- # F reference point unit - # F_start_year_ <- # start year of F plot - # F_end_year <- # start year of F plot - # F_units <- # units of F (plural) - # F_min <- # minimum F - # F_max <- # maximum F + # F.ref.pt <- # F reference point + # F.ref.pt.units <- # F reference point unit + # F.start.year. <- # start year of F plot + # F.end.year <- # start year of F plot + # F.units <- # units of F (plural) + # F.min <- # minimum F + # F.max <- # maximum F # Ftarg <- - # F_Ftarg <- + # F.Ftarg <- ## landings plot # start year of landings plot - landings_start_year <- dat |> + landings.start.year <- dat |> dplyr::filter( c(module_name == "t.series" & grepl("landings_observed", label)) | c(module_name == "CATCH" & grepl("ret_bio", label)), # t.series is associated with a conversion from BAM output and CATCH with SS3 converted output @@ -147,7 +146,7 @@ write_captions <- function(dat, # converted model output object as.numeric() # end year of landings plot - landings_end_year <- dat |> + landings.end.year <- dat |> dplyr::filter( c(module_name == "t.series" & grepl("landings_observed", label)) | c(module_name == "CATCH" & grepl("ret_bio", label)), # t.series is associated with a conversion from BAM output and CATCH with SS3 converted output @@ -161,11 +160,11 @@ write_captions <- function(dat, # converted model output object as.numeric() # units of landings (plural) - # landings_units <- # this will take some thought, since units is + # landings.units <- # this will take some thought, since units is # entered by the user in plot_landings.R # minimum landings - landings_min <- dat |> + landings.min <- dat |> dplyr::filter( c(module_name == "t.series" & grepl("landings_observed", label)) | c(module_name == "CATCH" & grepl("ret_bio", label)), # t.series is associated with a conversion from BAM output and CATCH with SS3 converted output @@ -181,7 +180,7 @@ write_captions <- function(dat, # converted model output object round(digits = 2) # maximum landings - landings_max <- dat |> + landings.max <- dat |> dplyr::filter( c(module_name == "t.series" & grepl("landings_observed", label)) | c(module_name == "CATCH" & grepl("ret_bio", label)), # t.series is associated with a conversion from BAM output and CATCH with SS3 converted output @@ -197,108 +196,108 @@ write_captions <- function(dat, # converted model output object round(digits = 2) ## natural mortality (M) - # M_age_min <- # minimum age of M - # M_age_max <- # maximum age of M - # M_units <- # units of M (plural) - # M_rate_min <- # minimum M rate - # M_rate_max <- # maximum M rate + # M.age.min <- # minimum age of M + # M.age.max <- # maximum age of M + # M.units <- # units of M (plural) + # M.rate.min <- # minimum M rate + # M.rate.max <- # maximum M rate ## vonB LAA (von Bertalanffy growth function + length at age) - # vonb_age_units <- # vonB age units (plural) - # vonb_age_min <- # minimum vonB age - # vonb_age_max <- # maximum vonB age - # vonb_length_units <- # vonB length units (plural) - # vonb_length_min <- # minimum vonB length - # vonb_length_max <- # minimum vonB length + # vonb.age.units <- # vonB age units (plural) + # vonb.age.min <- # minimum vonB age + # vonb.age.max <- # maximum vonB age + # vonb.length.units <- # vonB length units (plural) + # vonb.length.min <- # minimum vonB length + # vonb.length.max <- # minimum vonB length ## length-type conversion plot - # total_length_units <- # total length units (plural) - # total_length_min <- # minimum total length - # total_length_max <- # maximum total length - # fork_length_units <- # fork length units (plural) - # fork_length_min <- # minimum fork length - # fork_length_max <- # maximum fork length + # total.length.units <- # total length units (plural) + # total.length.min <- # minimum total length + # total.length.max <- # maximum total length + # fork.length.units <- # fork length units (plural) + # fork.length.min <- # minimum fork length + # fork.length.max <- # maximum fork length ## weight-length conversion plot - # wl_length_units <- # length units (plural) - # wl_length_min <- # minimum length - # wl_length_max <- # maximum length - # wl_weight_units <- # weight units (plural) - # wl_weight_min <- # minimum weight - # wl_weight_max <- # maximum weight + # wl.length.units <- # length units (plural) + # wl.length.min <- # minimum length + # wl.length.max <- # maximum length + # wl.weight.units <- # weight units (plural) + # wl.weight.min <- # minimum weight + # wl.weight.max <- # maximum weight ## maturity schedule (proportion mature) - # prop_mat_length_units <- # length units (plural) - # prop_mat_length_min <- # minimum length - # prop_mat_length_max <- # maximum length + # prop.mat.length.units <- # length units (plural) + # prop.mat.length.min <- # minimum length + # prop.mat.length.max <- # maximum length ## fecundity at length - # fecundity_length_units <- # length units (plural) - # fecundity_length_min <- # minimum length - # fecundity_length_max <- # maximum length - # fecundity_units <- # fecundity units (plural) - # fecundity_min <- # minimum fecundity - # fecundity_max <- # maximum fecundity + # fecundity.length.units <- # length units (plural) + # fecundity.length.min <- # minimum length + # fecundity.length.max <- # maximum length + # fecundity.units <- # fecundity units (plural) + # fecundity.min <- # minimum fecundity + # fecundity.max <- # maximum fecundity ## CAA (catch at age) - # fleet_or_survey_name <- # fleet or survey name (SHARED with CAL, below) - # caa_age_min <- # minimum age group - # caa_age_max <- # maximum age group + # fleet.or.survey.name <- # fleet or survey name (SHARED with CAL, below) + # caa.age.min <- # minimum age group + # caa.age.max <- # maximum age group ## CAL (catch at length) - # cal_length_min <- # minimum length group - # cal_length_max <- # maximum length group + # cal.length.min <- # minimum length group + # cal.length.max <- # maximum length group ## CPUE indices plot - # cpue_start_year <- # start year of CPUE indices plot - # cpue_end_year <- # end year of CPUE indices plot - # cpue_units <- # CPUE units (plural) (SHARED with mod_fit_abun, below) - # cpue_min <- # minimum CPUE (SHARED with mod_fit_abun, below) - # cpue_max <- # maximum CPUE (SHARED with mod_fit_abun, below) + # cpue.start.year <- # start year of CPUE indices plot + # cpue.end.year <- # end year of CPUE indices plot + # cpue.units <- # CPUE units (plural) (SHARED with mod.fit.abun, below) + # cpue.min <- # minimum CPUE (SHARED with mod_fit_abun, below) + # cpue.max <- # maximum CPUE (SHARED with mod_fit_abun, below) ## NAA (numbers at age) - # bubble_start_year_min <- # start year of NAA plot - # bubble_end_year_max <- # end year of NAA plot - # bubble_age_units <- # age units (plural) - # bubble_age_min <- # minimum age - # bubble_age_max <- # maximum age + # bubble.start.year.min <- # start year of NAA plot + # bubble.end.year.max <- # end year of NAA plot + # bubble.age.units <- # age units (plural) + # bubble.age.min <- # minimum age + # bubble.age.max <- # maximum age ## mod_fit_catch (model fit to catch ts) - # mod_fit_catch_start_year <- # start year of model fit to catch ts plot - # mod_fit_catch_end_year <- # end year of model fit to catch ts plot - # mod_fit_catch_units <- # catch units (plural) - # mod_fit_catch_min <- # minimum catch - # mod_fit_catch_max <- # maximum catch + # mod.fit.catch.start.year <- # start year of model fit to catch ts plot + # mod.fit.catch.end.year <- # end year of model fit to catch ts plot + # mod.fit.catch.units <- # catch units (plural) + # mod.fit.catch.min <- # minimum catch + # mod.fit.catch.max <- # maximum catch ## mod_fit_abun (model fit to abundance indices plot) - # mod_fit_abun_start_year <- # start year of model fit to abundance indices plot - # mod_fit_abun_end_year <- # end year of model fit to abundance indices plot + # mod.fit.abun.start.year <- # start year of model fit to abundance indices plot + # mod.fit.abun.end.year <- # end year of model fit to abundance indices plot ## mod_fit_discards - # mod_fit_discards_start_year <- # start year of model fit to discards plot - # mod_fit_discards_end_year <- # end year of model fit to discards plot - # mod_fit_discards_units <- # discards units (plural) - # mod_fit_discards_min <- # minimum discards - # mod_fit_discards_max <- # maximum discards + # mod.fit.discards.start.year <- # start year of model fit to discards plot + # mod.fit.discards.end.year <- # end year of model fit to discards plot + # mod.fit.discards.units <- # discards units (plural) + # mod.fit.discards.min <- # minimum discards + # mod.fit.discards.max <- # maximum discards ## selectivity - # selectivity_start_year <- # start year of selectivity plot - # selectivity_end_year <- # end year of selectivity plot - # selectivity_length_units <- # length units (plural) - # selectivity_length_min <- # minimum length - # selectivity_length_max <- # maximum length + # selectivity.start.year <- # start year of selectivity plot + # selectivity.end.year <- # end year of selectivity plot + # selectivity.length.units <- # length units (plural) + # selectivity.length.min <- # minimum length + # selectivity.length.max <- # maximum length ## estimated stock recruitment (aka spawning stock biomass) # youngest-age recruited fish (instead of age-0) - # sr_age_min <- # unsure how to extract this + # sr.age.min <- # unsure how to extract this # ssb units (plural) - # sr_ssb_units <- # this will take some thought, since + # sr.ssb.units <- # this will take some thought, since # spawning_biomass_label is entered by the user in plot_spawn_recruitment.R # minimum ssb - sr_ssb_min <- dat |> + sr.ssb.min <- dat |> dplyr::filter(label == "spawning_biomass", module_name == "TIME_SERIES" | module_name == "t.series", !is.na(year), @@ -316,7 +315,7 @@ write_captions <- function(dat, # converted model output object round(digits = 2) # maximum ssb - sr_ssb_max <- dat |> + sr.ssb.max <- dat |> dplyr::filter(label == "spawning_biomass", module_name == "TIME_SERIES" | module_name == "t.series", !is.na(year), @@ -334,11 +333,11 @@ write_captions <- function(dat, # converted model output object round(digits = 2) # recruitment units (plural) - # sr_units <- # this will take some thought, since recruitment_label + # sr.units <- # this will take some thought, since recruitment_label # is entered by the user in plot_spawn_recruitment.R # minimum recruitment - sr_min <- dat |> + sr.min <- dat |> dplyr::filter(label == "recruitment", module_name == "TIME_SERIES" | module_name == "t.series", !is.na(year), @@ -356,7 +355,7 @@ write_captions <- function(dat, # converted model output object round(digits = 2) # maximum recruitment - sr_max <- dat |> + sr.max <- dat |> dplyr::filter(label == "recruitment", module_name == "TIME_SERIES" | module_name == "t.series", !is.na(year), @@ -373,23 +372,14 @@ write_captions <- function(dat, # converted model output object as.numeric() |> round(digits = 2) - ## relative recruitment - # minimum relative recruitment - rel_recruitment_min <- (recruitment_min / R0) |> - round(digits = 2) - - # maximum relative recruitment - rel_recruitment_max <- (recruitment_max / R0) |> - round(digits = 2) - ## recruitment ts # recruitment units (plural) - numbers of fish, in thousands - # recruitment_units <- # this will take some thought, since unit_label is + # recruitment.units <- # this will take some thought, since unit_label is # entered by the user in plot_recruitment.R # start year of recruitment ts plot - recruitment_start_year <- dat |> + recruitment.start.year <- dat |> dplyr::filter(label == "recruitment", module_name == "TIME_SERIES" | module_name == "t.series", !is.na(year), @@ -406,18 +396,29 @@ write_captions <- function(dat, # converted model output object as.numeric() # end year of recruitment ts plot - # recruitment_end_year <- # this will take some thought, since end_year is + # recruitment.end.year <- # this will take some thought, since end_year is # either entered by the user or calculated in plot_recruitment.R # minimum recruitment - recruitment_min <- sr_min + recruitment.min <- sr.min # maximum recruitment - recruitment_max <- sr_max + recruitment.max <- sr.max + + + ## relative recruitment + # minimum relative recruitment + rel.recruitment.min <- (recruitment.min / R0) |> + round(digits = 2) + + # maximum relative recruitment + rel.recruitment.max <- (recruitment.max / R0) |> + round(digits = 2) + ## recruitment deviations # start year of recruitment deviations plot - recruit_dev_start_year <- dat |> + recruit.dev.start.year <- dat |> dplyr::filter(label == "recruitment_deviations" | label == "log_recruitment_deviations", module_name == "SPAWN_RECRUIT" | module_name == "t.series", !is.na(year), @@ -434,11 +435,11 @@ write_captions <- function(dat, # converted model output object as.numeric() # end year of recruitment deviations plot - # recruit_dev_end_year <- # this will take some thought, since end_year is + # recruit.dev.end.year <- # this will take some thought, since end_year is # either entered by the user or calculated in plot_recruitment_deviations.R # minimum recruitment deviation - recruit_dev_min <- dat |> + recruit.dev.min <- dat |> dplyr::filter(label == "recruitment_deviations" | label == "log_recruitment_deviations", module_name == "SPAWN_RECRUIT" | module_name == "t.series", !is.na(year), @@ -456,7 +457,7 @@ write_captions <- function(dat, # converted model output object round(digits = 2) # maximum recruitment deviation - recruit_dev_max <- dat |> + recruit.dev.max <- dat |> dplyr::filter(label == "recruitment_deviations" | label == "log_recruitment_deviations", module_name == "SPAWN_RECRUIT" | module_name == "t.series", !is.na(year), @@ -472,17 +473,17 @@ write_captions <- function(dat, # converted model output object round(digits = 2) ## tot_b (total biomass) - # biomass_start_year <- # start year of biomass plot - # biomass_end_year <- # end year of biomass plot - # biomass_units <- # biomass units (plural) - # biomass_min <- # minimum biomass - # biomass_max <- # maximum biomass - # biomass_ref_pt <- # biomass reference point - # biomass_ref_pt_units <- # biomass reference point units + # biomass.start.year <- # start year of biomass plot + # biomass.end.year <- # end year of biomass plot + # biomass.units <- # biomass units (plural) + # biomass.min <- # minimum biomass + # biomass.max <- # maximum biomass + # biomass.ref.pt <- # biomass reference point + # biomass.ref.pt.units <- # biomass reference point units ## spawning_biomass (ssb) # start year of ssb plot - ssb_start_year <- dat |> + ssb.start.year <- dat |> dplyr::filter( label == "spawning_biomass", module_name %in% c("DERIVED_QUANTITIES", "t.series") @@ -496,15 +497,15 @@ write_captions <- function(dat, # converted model output object round(digits = 2) # end year of ssb plot - # ssb_end_year <- # this will take some thought, since end_year is + # ssb.end.year <- # this will take some thought, since end_year is # either entered by the user or calculated in plot_spawning_biomass.R # ssb units (plural) - # ssb_units <- # this will take some thought, since unit_label is + # ssb.units <- # this will take some thought, since unit_label is # entered by the user in plot_spawning_biomass.R # minimum ssb - ssb_min <- dat |> + ssb.min <- dat |> dplyr::filter( label == "spawning_biomass", module_name %in% c("DERIVED_QUANTITIES", "t.series") @@ -518,7 +519,7 @@ write_captions <- function(dat, # converted model output object round(digits = 2) # maximum ssb - ssb_max <- dat |> + ssb.max <- dat |> dplyr::filter( label == "spawning_biomass", module_name %in% c("DERIVED_QUANTITIES", "t.series") @@ -532,11 +533,11 @@ write_captions <- function(dat, # converted model output object round(digits = 2) # ssb reference point - # ssb_ref_pt <- # this will take some thought, since ref_line_val is + # ssb.ref.pt <- # this will take some thought, since ref_line_val is # calculated in plot_spawning_biomass.R # ssb reference point units - # ssb_ref_pt_units <- ssb_units + # ssb.ref.pt.units <- ssb_units ssbtarg <- dat |> dplyr::filter(c(grepl('spawning_biomass', label) & grepl('msy$', label) & estimate >1) | label == 'spawning_biomass_msy$') |> @@ -546,46 +547,46 @@ write_captions <- function(dat, # converted model output object ## relative ssb # relative ssb min - rel_ssb_min <- (ssb_min / ssbtarg) |> + rel.ssb.min <- (ssb.min / ssbtarg) |> round(digits = 2) # relative ssb max - rel_ssb_max <- (ssb_max / ssbtarg) |> + rel.ssb.max <- (ssb.max / ssbtarg) |> round(digits = 2) ## spr (spawning potential ratio) - # spr_start_year <- # start year of spr plot - # spr_end_year <- # end year of spr plot - # spr_min <- # minimum spr - # spr_max <- # maximum spr - # spr_ref_pt <- # spr reference point - # spr_ref_pt_units <- # spr reference point units + # spr.start.year <- # start year of spr plot + # spr.end.year <- # end year of spr plot + # spr.min <- # minimum spr + # spr.max <- # maximum spr + # spr.ref.pt <- # spr reference point + # spr.ref.pt.units <- # spr reference point units ## pop_naa_baa (population numbers at age and population biomass at age) - # pop_naa_baa_start_year <- # start year of spr plot - # pop_naa_baa_end_year <- # end year of spr plot - # pop_naa_baa_fish_min <- # minimum number of fish - # pop_naa_baa_fish_max <- # maximum number of fish + # pop.naa.baa.start.year <- # start year of spr plot + # pop.naa.baa.end.year <- # end year of spr plot + # pop.naa.baa.fish.min <- # minimum number of fish + # pop.naa.baa.fish.max <- # maximum number of fish ## proj_catch (projected catch) - # proj_catch_units <- # projected catch units (plural) - # proj_catch_start_year <- # start year of projected catch plot - # proj_catch_end_year <- # end year of projected catch plot - # proj_catch_min <- # minimum projected catch - # proj_catch_max <- # maximum projected catch + # proj.catch.units <- # projected catch units (plural) + # proj.catch.start.year <- # start year of projected catch plot + # proj.catch.end.year <- # end year of projected catch plot + # proj.catch.min <- # minimum projected catch + # proj.catch.max <- # maximum projected catch ## proj_biomass (projected biomass) - # proj_biomass_units <- # projected biomass units (plural) - # proj_biomass_start_year <- # start year of projected biomass plot - # proj_biomass_end_year <- # end year of projected biomass plot - # proj_biomass_min <- # minimum projected biomass - # proj_biomass_max <- # maximum projected biomass - # proj_biomass_ref_pt <- # projected biomass reference point - # proj_biomass_ref_pt_units <- # projected biomass reference point units + # proj.biomass.units <- # projected biomass units (plural) + # proj.biomass.start.year <- # start year of projected biomass plot + # proj.biomass.end.year <- # end year of projected biomass plot + # proj.biomass.min <- # minimum projected biomass + # proj.biomass.max <- # maximum projected biomass + # proj.biomass.ref.pt <- # projected biomass reference point + # proj.biomass.ref.pt.units <- # projected biomass reference point units ## Other - # tot_catch <- + # tot.catch <- # M <- # steep <- # SBmsy <- @@ -594,16 +595,16 @@ write_captions <- function(dat, # converted model output object # TABLES----- ## catch - # catch_fleet <- # fleet + # catch.fleet <- # fleet ## landings - # landings_tbl_units <- # landings units; remove if units already in table + # landings.tbl.units <- # landings units; remove if units already in table ## discards - # discards_tbl_units <- # discards units + # discards.tbl.units <- # discards units ## catchability - # catchability_fleet <- # fleet + # catchability.fleet <- # fleet # add in more quantities here, and update the quantities above @@ -618,231 +619,231 @@ write_captions <- function(dat, # converted model output object # FIGURES----- ## kobe plot - # 'B_BMSY_min' = B_BMSY_min, - # 'B_BMSY_max' = B_BMSY_max, - # 'F_FMSY_min' = F_FMSY_min, - # 'F_FMSY_max' = F_FMSY_max, - # 'B_BMSY_end_yr' = B_BMSY_end_yr, - # 'F_FMSY_end_yr' = F_FMSY_end_yr, - # 'overfished_status_is_isnot' = overfished_status_is_isnot, - # 'overfishing_status_is_isnot' = overfishing_status_is_isnot, - # 'kobe_start_year' = kobe_start_year, - # 'kobe_end_year' = kobe_end_year, + # 'B.BMSY.min' = B.BMSY.min, + # 'B.BMSY.max' = B.BMSY.max, + # 'F.FMSY.min' = F.FMSY.min, + # 'F.FMSY.max' = F.FMSY.max, + # 'B.BMSY.end.yr' = B.BMSY.end.yr, + # 'F.FMSY.end.yr' = F.FMSY.end.yr, + # 'overfished.status.is.isnot' = overfished.status.is.isnot, + # 'overfishing.status.is.isnot' = overfishing.status.is.isnot, + # 'kobe.start.year' = kobe.start.year, + # 'kobe.end.year' = kobe.end.year, ## Relative biomass plot - # NOTE: moving this above biomass so rel_B_min isn't changed to "rel_" + B_min (etc.) - 'rel_B_min' = rel_B_min, - 'rel_B_max' = rel_B_max, + # NOTE: moving this above biomass so rel.B.min isn't changed to "rel." + B.min (etc.) + 'rel.B.min' = rel.B.min, + 'rel.B.max' = rel.B.max, ## Biomass plot - # 'B_ref_pt' = B_ref_pt, - # 'B_ref_pt_units' = B_ref_pt_units, - 'B_start_year' = B_start_year, - # 'B_end_year' = B_end_year, - # 'B_units' = B_units, - 'B_min' = B_min, - 'B_max' = B_max, + # 'B.ref.pt' = B.ref.pt, + # 'B.ref.pt.units' = B.ref.pt.units, + 'B.start.year' = B.start.year, + # 'B.end.year' = B.end.year, + # 'B.units' = B.units, + 'B.min' = B.min, + 'B.max' = B.max, 'R0' = R0, # 'Bend' = Bend, 'Btarg' = Btarg, # 'Bmsy' = Bmsy, ## mortality (F) plot - # 'F_ref_pt' = F_ref_pt, - # 'F_ref_pt_units' = F_ref_pt_units, - # 'F_start_year' = F_start_year, - # 'F_end_year' = F_end_year, - # 'F_units' = F_units, - # 'F_min' = F_min, - # 'F_max' = F_max, + # 'F.ref.pt' = F.ref.pt, + # 'F.ref.pt.units' = F.ref.pt.units, + # 'F.start.year' = F.start.year, + # 'F.end.year' = F.end.year, + # 'F.units' = F.units, + # 'F.min' = F.min, + # 'F.max' = F.max, # 'Ftarg' = Ftarg, - # 'F_Ftarg' = F_Ftarg, + # 'F.Ftarg' = F.Ftarg, ## landings plot - 'landings_start_year' = landings_start_year, - 'landings_end_year' = landings_end_year, - # 'landings_units' = landings_units, - 'landings_min' = landings_min, - 'landings_max' = landings_max, + 'landings.start.year' = landings.start.year, + 'landings.end.year' = landings.end.year, + # 'landings.units' = landings.units, + 'landings.min' = landings.min, + 'landings.max' = landings.max, ## natural mortality (M) - # 'M_age_min' = M_age_min, - # 'M_age_max' = M_age_max, - # 'M_units' = M_units, - # 'M_rate_min' = M_rate_min, - # 'M_rate_max' = M_rate_max, + # 'M.age.min' = M.age.min, + # 'M.age.max' = M.age.max, + # 'M.units' = M.units, + # 'M.rate.min' = M.rate.min, + # 'M.rate.max' = M.rate.max, ## vonB LAA (von Bertalanffy growth function + length at age) - # 'vonb_age_units' = vonb_age_units, - # 'vonb_age_min' = vonb_age_min, - # 'vonb_age_max' = vonb_age_max, - # 'vonb_length_units' = vonb_length_units, - # 'vonb_length_min' = vonb_length_min, - # 'vonb_length_max' = vonb_length_max, + # 'vonb.age.units' = vonb.age.units, + # 'vonb.age.min' = vonb.age.min, + # 'vonb.age.max' = vonb.age.max, + # 'vonb.length.units' = vonb.length.units, + # 'vonb.length.min' = vonb.length.min, + # 'vonb.length.max' = vonb.length.max, ## length-type conversion plot - # 'total_length_units' = total_length_units, - # 'total_length_min' = total_length_min, - # 'total_length_max' = total_length_max, - # 'fork_length_units' = fork_length_units, - # 'fork_length_min' = fork_length_min, - # 'fork_length_max' = fork_length_max, + # 'total.length.units' = total.length.units, + # 'total.length.min' = total.length.min, + # 'total.length.max' = total.length.max, + # 'fork.length.units' = fork.length.units, + # 'fork.length.min' = fork.length.min, + # 'fork.length.max' = fork.length.max, ## weight-length conversion plot - # 'wl_length_units' = wl_length_units, - # 'wl_length_min' = wl_length_min, - # 'wl_length_max' = wl_length_max, - # 'wl_weight_units' = wl_weight_units, - # 'wl_weight_min' = wl_weight_min, - # 'wl_weight_max' = wl_weight_max, + # 'wl.length.units' = wl.length.units, + # 'wl.length.min' = wl.length.min, + # 'wl.length.max' = wl.length.max, + # 'wl.weight.units' = wl.weight.units, + # 'wl.weight.min' = wl.weight.min, + # 'wl.weight.max' = wl.weight.max, ## maturity schedule (proportion mature) - # 'prop_mat_length_units' = prop_mat_length_units, - # 'prop_mat_length_min' = prop_mat_length_min, - # 'prop_mat_length_max' = prop_mat_length_max, + # 'prop.mat.length.units' = prop.mat.length.units, + # 'prop.mat.length.min' = prop.mat.length.min, + # 'prop.mat.length.max' = prop.mat.length.max, ## fecundity at length - # 'fecundity_length_units' = fecundity_length_units, - # 'fecundity_length_min' = fecundity_length_min, - # 'fecundity_length_max' = fecundity_length_max, - # 'fecundity_units' = fecundity_units, - # 'fecundity_min' = fecundity_min, - # 'fecundity_max' = fecundity_max, + # 'fecundity.length.units' = fecundity.length.units, + # 'fecundity.length.min' = fecundity.length.min, + # 'fecundity.length.max' = fecundity.length.max, + # 'fecundity.units' = fecundity.units, + # 'fecundity.min' = fecundity.min, + # 'fecundity.max' = fecundity.max, ## CAA (catch at age) - # 'fleet_or_survey_name' = fleet_or_survey_name, - # 'caa_age_min' = caa_age_min, - # 'caa_age_max' = caa_age_max, + # 'fleet.or.survey.name' = fleet.or.survey.name, + # 'caa.age.min' = caa.age.min, + # 'caa.age.max' = caa.age.max, ## CAL (catch at length) - # 'cal_length_min' = cal_length_min, - # 'cal_length_max' = cal_length_max, + # 'cal.length.min' = cal.length.min, + # 'cal.length.max' = cal.length.max, ## CPUE indices plot - # 'cpue_start_year' = cpue_start_year, - # 'cpue_end_year' = cpue_end_year, - # 'cpue_units' = cpue_units, - # 'cpue_min' = cpue_min, - # 'cpue_max' = cpue_max, + # 'cpue.start.year' = cpue.start.year, + # 'cpue.end.year' = cpue.end.year, + # 'cpue.units' = cpue.units, + # 'cpue.min' = cpue.min, + # 'cpue.max' = cpue.max, ## NAA (numbers at age) - # 'bubble_start_year_min' = bubble_start_year_min, - # 'bubble_end_year_max' = bubble_end_year_max, - # 'bubble_age_units' = bubble_age_units, - # 'bubble_age_min' = bubble_age_min, - # 'bubble_age_max' = bubble_age_max, + # 'bubble.start.year.min' = bubble.start.year.min, + # 'bubble.end.year.max' = bubble.end.year.max, + # 'bubble.age.units' = bubble.age.units, + # 'bubble.age.min' = bubble.age.min, + # 'bubble.age.max' = bubble.age.max, ## mod_fit_catch (model fit to catch ts) - # 'mod_fit_catch_start_year' = mod_fit_catch_start_year, - # 'mod_fit_catch_end_year' = mod_fit_catch_end_year, - # 'mod_fit_catch_units' = mod_fit_catch_units, - # 'mod_fit_catch_min' = mod_fit_catch_min, - # 'mod_fit_catch_max' = mod_fit_catch_max, + # 'mod.fit.catch.start.year' = mod.fit.catch.start.year, + # 'mod.fit.catch.end.year' = mod.fit.catch.end.year, + # 'mod.fit.catch.units' = mod.fit.catch.units, + # 'mod.fit.catch.min' = mod.fit.catch.min, + # 'mod.fit.catch.max' = mod.fit.catch.max, ## mod_fit_abun (model fit to abundance indices plot) - # 'mod_fit_abun_start_year' = mod_fit_abun_start_year, - # 'mod_fit_abun_end_year' = mod_fit_abun_end_year, + # 'mod.fit.abun.start.year' = mod.fit.abun.start.year, + # 'mod.fit.abun.end.year' = mod.fit.abun.end.year, ## mod_fit_discards - # 'mod_fit_discards_start_year' = mod_fit_discards_start_year, - # 'mod_fit_discards_end_year' = mod_fit_discards_end_year, - # 'mod_fit_discards_units' = mod_fit_discards_units, - # 'mod_fit_discards_min' = mod_fit_discards_min, - # 'mod_fit_discards_max' = mod_fit_discards_max, + # 'mod.fit.discards.start.year' = mod.fit.discards.start.year, + # 'mod.fit.discards.end.year' = mod.fit.discards.end.year, + # 'mod.fit.discards.units' = mod.fit.discards.units, + # 'mod.fit.discards.min' = mod.fit.discards.min, + # 'mod.fit.discards.max' = mod.fit.discards.max, ## selectivity - # 'selectivity_start_year' = selectivity_start_year, - # 'selectivity_end_year' = selectivity_end_year, - # 'selectivity_length_units' = selectivity_length_units, - # 'selectivity_length_min' = selectivity_length_min, - # 'selectivity_length_max' = selectivity_length_max, + # 'selectivity.start.year' = selectivity.start.year, + # 'selectivity.end.year' = selectivity.end.year, + # 'selectivity.length.units' = selectivity.length.units, + # 'selectivity.length.min' = selectivity.length.min, + # 'selectivity.length.max' = selectivity.length.max, ## estimated stock recruitment (aka spawning stock biomass) - # 'sr_age_min' = sr_age_min, - # 'sr_ssb_units' = sr_ssb_units, - 'sr_ssb_min' = sr_ssb_min, - 'sr_ssb_max' = sr_ssb_max, - # 'sr_units' = sr_units, - 'sr_min' = sr_min, - 'sr_max' = sr_max, + # 'sr.age.min' = sr.age.min, + # 'sr.ssb.units' = sr.ssb.units, + 'sr.ssb.min' = sr.ssb.min, + 'sr.ssb.max' = sr.ssb.max, + # 'sr.units' = sr.units, + 'sr.min' = sr.min, + 'sr.max' = sr.max, # relative recruitment ts - # NOTE: moving this above recruitment so rel_recruitment_min isn't changed - # to "rel_" + recruitment_min (etc.) - 'rel_recruitment_min' = rel_recruitment_min, - 'rel_recruitment_max' = rel_recruitment_max, + # NOTE: moving this above recruitment so rel.recruitment.min isn't changed + # to "rel." + recruitment.min (etc.) + 'rel.recruitment.min' = rel.recruitment.min, + 'rel.recruitment.max' = rel.recruitment.max, ## recruitment ts - # 'recruitment_units' = recruitment_units, - 'recruitment_start_year' = recruitment_start_year, - # 'recruitment_end_year' = recruitment_end_year, - 'recruitment_min' = recruitment_min, - 'recruitment_max' = recruitment_max, + # 'recruitment.units' = recruitment.units, + 'recruitment.start.year' = recruitment.start.year, + # 'recruitment.end.year' = recruitment.end.year, + 'recruitment.min' = recruitment.min, + 'recruitment.max' = recruitment.max, ## recruitment deviations - 'recruit_dev_start_year' = recruit_dev_start_year, - # 'recruit_dev_end_year' = recruit_dev_end_year, - 'recruit_dev_min' = recruit_dev_min, - 'recruit_dev_max' = recruit_dev_max, + 'recruit.dev.start.year' = recruit.dev.start.year, + # 'recruit.dev.end.year' = recruit.dev.end.year, + 'recruit.dev.min' = recruit.dev.min, + 'recruit.dev.max' = recruit.dev.max, ## tot_b (total biomass) - # 'biomass_start_year' = biomass_start_year, - # 'biomass_end_year' = biomass_end_year, - # 'biomass_units' = biomass_units, - # 'biomass_min' = biomass_min, - # 'biomass_max' = biomass_max, - # 'biomass_ref_pt' = biomass_ref_pt, - # 'biomass_ref_pt_units' = biomass_ref_pt_units, + # 'biomass.start.year' = biomass.start.year, + # 'biomass.end.year' = biomass.end.year, + # 'biomass.units' = biomass.units, + # 'biomass.min' = biomass.min, + # 'biomass.max' = biomass.max, + # 'biomass.ref.pt' = biomass.ref.pt, + # 'biomass.ref.pt.units' = biomass.ref.pt.units, # relative ssb - # NOTE: moving this above recruitment so rel_ssb_min isn't changed to - # "rel_" + ssb_min, etc. - 'rel_ssb_min' = rel_ssb_min, - 'rel_ssb_max' = rel_ssb_max, - - ## spawning_biomass (ssb) - 'ssb_start_year' = ssb_start_year, - # 'ssb_end_year' = ssb_end_year, - # 'ssb_units' = ssb_units, - 'ssb_min' = ssb_min, - 'ssb_max' = ssb_max#, - # 'ssb_ref_pt' = ssb_ref_pt, - # 'ssb_ref_pt_units' = ssb_ref_pt_units, + # NOTE: moving this above recruitment so rel.ssb.min isn't changed to + # "rel." + ssb.min, etc. + 'rel.ssb.min' = rel.ssb.min, + 'rel.ssb.max' = rel.ssb.max, + + ## spawning.biomass (ssb) + 'ssb.start.year' = ssb.start.year, + # 'ssb.end.year' = ssb.end.year, + # 'ssb.units' = ssb.units, + 'ssb.min' = ssb.min, + 'ssb.max' = ssb.max#, + # 'ssb.ref.pt' = ssb.ref.pt, + # 'ssb.ref.pt.units' = ssb.ref.pt.units, # 'ssbtarg' = ssbtarg, # ## spr (spawning potential ratio) - # 'spr_start_year' = spr_start_year, - # 'spr_end_year' = spr_end_year, - # 'spr_min' = spr_min, - # 'spr_max' = spr_max, - # 'spr_ref_pt' = spr_ref_pt, - # 'spr_ref_pt_units' = spr_ref_pt_units, + # 'spr.start.year' = spr.start.year, + # 'spr.end.year' = spr.end.year, + # 'spr.min' = spr.min, + # 'spr.max' = spr.max, + # 'spr.ref.pt' = spr.ref.pt, + # 'spr.ref.pt.units' = spr.ref.pt.units, # # ## pop_naa_baa (population numbers at age and population biomass at age) - # 'pop_naa_baa_start_year' = pop_naa_baa_start_year, - # 'pop_naa_baa_end_year' = pop_naa_baa_end_year, - # 'pop_naa_baa_fish_min' = pop_naa_baa_fish_min, - # 'pop_naa_baa_fish_max' = pop_naa_baa_fish_max, + # 'pop.naa.baa.start.year' = pop.naa.baa.start.year, + # 'pop.naa.baa.end.year' = pop.naa.baa.end.year, + # 'pop.naa.baa.fish.min' = pop.naa.baa.fish.min, + # 'pop.naa.baa.fish.max' = pop.naa.baa.fish.max, # # ## proj_catch (projected catch) - # 'proj_catch_units' = proj_catch_units, - # 'proj_catch_start_year' = proj_catch_start_year, - # 'proj_catch_end_year' = proj_catch_end_year, - # 'proj_catch_min' = proj_catch_min, - # 'proj_catch_max' = proj_catch_max, + # 'proj.catch.units' = proj.catch.units, + # 'proj.catch.start.year' = proj.catch.start.year, + # 'proj.catch.end.year' = proj.catch.end.year, + # 'proj.catch.min' = proj.catch.min, + # 'proj.catch.max' = proj.catch.max, # # ## proj_biomass (projected biomass) - # 'proj_biomass_units' = proj_biomass_units, - # 'proj_biomass_start_year' = proj_biomass_start_year, - # 'proj_biomass_end_year' = proj_biomass_end_year, - # 'proj_biomass_min' = proj_biomass_min, - # 'proj_biomass_max' = proj_biomass_max, - # 'proj_biomass_ref_pt' = proj_biomass_ref_pt, - # 'proj_biomass_ref_pt_units' = proj_biomass_ref_pt_units, + # 'proj.biomass.units' = proj.biomass.units, + # 'proj.biomass.start.year' = proj.biomass.start.year, + # 'proj.biomass.end.year' = proj.biomass.end.year, + # 'proj.biomass.min' = proj.biomass.min, + # 'proj.biomass.max' = proj.biomass.max, + # 'proj.biomass.ref.pt' = proj.biomass.ref.pt, + # 'proj.biomass.ref.pt.units' = proj.biomass.ref.pt.units, # # ## Other - # 'tot_catch' = tot_catch, + # 'tot.catch' = tot.catch, # 'M' = M, # 'steep' = steep, # 'SBmsy' = SBmsy, @@ -852,16 +853,16 @@ write_captions <- function(dat, # converted model output object # # TABLES----- # # ## catch - # 'catch_fleet' = catch_fleet, + # 'catch.fleet' = catch.fleet, # # ## landings - # 'landings_tbl_units' = landings_tbl_units, + # 'landings.tbl.units' = landings.tbl.units, # # ## discards - # 'discards_tbl_units' = discards_tbl_units, + # 'discards.tbl.units' = discards.tbl.units, # # ## catchability - # 'catchability_fleet' = catchability_fleet + # 'catchability.fleet' = catchability.fleet ) # take the values associated with the quantities and replace the df's diff --git a/inst/resources/captions_alt_text_template.csv b/inst/resources/captions_alt_text_template.csv index f2131eb..a326b61 100644 --- a/inst/resources/captions_alt_text_template.csv +++ b/inst/resources/captions_alt_text_template.csv @@ -1,47 +1,47 @@ label,type,caption,alt_text -kobe,figure,"Kobe plot showing stock status. Triangles delineate start and end years. Horizontal and vertical dashed lines delineate the proportion of F/F~MSY~ where F~MSY~ = B_ref_pt, and B/B~MSY~ where B~MSY~ = B_ref_pt. Overfishing is occurring when F/F~MSY~ > 1 and an overfished status is indicated where B/B~MSY~ > 1.","A Kobe plot showing stock status from kobe_start_year to kobe_end_year. The x axis, showing overfished status (i.e., B/B~MSY~), spans from B_BMSY_min to B_BMSY_max and the y axis, showing overfishing (i.e., F/F~MSY~), spans from F_FMSY_min to F_FMSY_max. The B/B~MSY~ and F/F~MSY~ for end_year_kobe were B_BMSY_end_yr and F_FMSY_end_yr, respectively, indicating that the stock overfished_status_is_isnot overfished and overfishing_status_is_is_not experiencing overfishing." -biomass,figure,Biomass (B) time series. The horizontal dashed line represents the limit reference point (B_ref_pt B_ref_pt_units).,"Line graph showing biomass time series. The x axis, showing the year, spans from B_start_year to B_end_year and the y axis, showing biomass in B_units, spans from B_min to B_max." -relative_biomass,figure,"Relative biomass (B) time series. The horizontal dashed line represents the limit reference point calculated as B/B(reference point), where B(reference point) is B_ref_point B_ref_pt_units.","Line graph showing relative biomass time series. The x axis, showing the year, spans from B_start_year to B_end_year and the y axis, showing relative biomass (B/B~target~), spans from rel_B_min to rel_B_max." -fishing_mortality,figure,Fishing mortality (F) over time. The horizontal dashed line represents the target reference point (F_ref_pt F_ref_pt_unit).,"Line graph showing fishing mortality over time . The x axis, showing the year, spans from F_start_year to F_end_year and the y axis, showing fishing mortality in F_units, spans from F_min to F_max." -landings,figure,Historical landings by fleet.,"Cumulative area plot showing historical landings. The x axis, showing the year, spans from landings_start_year to landings_end_year and the y axis, showing landings in landings_units, spans from landings_min to landings_max." -natural_mortality,figure,Natural mortality (M) for each age. ,"Line graph showing natural mortality. The x axis, showing age in M_units, spans from M_age_min to M_age_max and the y axis, showing the natural mortality rate per year, spans from M_rate_min to M_rate_max." -vonb_laa,figure,Aged and measured fish (points) and von Bertalanffy growth function (line) fit to the data.,"Point and line graph showing observations of measured age and length data as points and the von Bertalanffy relationship fit to this data as a line with 95% confidence intervals. The x axis, showing age in vonb_age_units, spans from vonb_age_min to vonb_age_max, and the y axis, showing length in vonb_length_units, spans from vonb_length_min to vonb_length_max." -length_type_conversion,figure,Length-type conversion relationship between total and fork length where points represent individual fish length measurement observations and the line is the fitted relationship.,"Point and line graph showing observations of measured fork length and measured total length from the same fish for conversion purposes as points, and a linear fit through those points as a line. The x axis, showing total length in total_length_units, spans from total_length_min to total_length_max and the y axis, showing fork length in fork_length_units, spans from fork_length_min to fork_length_max." -weight_length_converstion,figure,Weight-length conversion relationship where the points represent individual fish observations and the line is the fitted relationship. ,"Point and line graph showing observations of measured length and measured weight from the same fish for conversion purposes as points, and an exponential fit through those points as a line. The x axis, showing length in wl_length_units, spans from wl_length_min to wl_length_max, and the y axis, showing weight in wl_weight_units, spans from wl_weight_min to wl_weight_max." -maturity_schedule,figure,The relationship between the proportion mature and fish length. ,"Graph showing the relationship between fish maturity and length. Points, if present, show observations of maturity at different fish lengths and the line represents either the fit to the points, or the assumed or known maturity schedule. The x axis, showing length in prop_mat_length_units, spans from prop_mat_length_min to prop_mat_length_max and the y axis, showing the proportion mature, spans from 0--1." -fecundity_at_length,figure,Fecundity (in number of eggs) as a function of fish length. ,"Point and line graph showing observations of measured fecundity and measured length from the same fish and an exponential fit through those points displayed as a line. The x axis, showing length in fecundity_length_units, spans from fecundity_length_min to fecundity_length_max, and the y axis, showing fecundity in fecundity_units, spans from fecundity_min to fecundity_max." -CAA,figure,"Histograms showing the proportion of the catch in each age group for each year in which there is composition data, for fleet or survey fleet_or_survey_name.","Histograms for each year and fleet for which there is data (one per year grouped by fleet or survey), which show the proportion of the catch in each age group. The x axis of each histogram, showing age groups, span from caa_age_min to caa_age_max, while the y axis of each histogram, showing the proportion of the catch, spans from 0--1." -CAL,figure,"Histograms showing the proportion of the catch in each length group, each year for which there is composition data, for fleet or survey fleet_or_survey_name.","Histograms for each year and fleet for which there is data (one per year grouped by fleet or survey), which show the proportion of the catch in each length group. The x axis of each histogram contains length intervals that span from cal_length_min to cal_length_max, while the y axis of each histogram contains the proportion of the catch, which span from 0--1." -CPUE_indices,figure,Catch per unit effort (CPUE) over time for fleet or survey. 95% confidence intervals are shown for each survey/fleet.,"Line graph showing catch per unit effort (CPUE) over time for fleet or survey from cpue_start_year to cpue_end_year, stratified by survey/fleet. The x axis, showing the year, spans from cpue_start_year to cpue_end_year, and the y axis, showing CPUE in cpue_units, spans from cpue_min to cpue_max." -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." -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." -sr,figure,Stock recruitment relationship estimated by the assessment model. ,"Point and line graph showing the relationship between spawning stock biomass and newly recruited sr_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 sr_ssb_units, spans from sr_ssb_min to sr_ssb_max, while the y axis, showing recruitment in sr_units, spans from sr_min to sr_max." -recruitment,figure,Estimated recruitment by the assessment model each year in recruitment_units.,"Line graph showing the assessment model estimated recruitment in sr_units for each year. The x axis, showing years, spans from recruitment_start_year to recruitment_end_year, while the y axis, showing recruitment in recruitment_units, spans from recruitment_min to recruitment_max." -relative_recruitment,figure,"Estimated relative recruitment by the assessment model each year in recruitment_units, calculated as R/R~0~ where R~0~ is R0.","Line graph showing the assessment model estimated relative recruitment in sr_units for each year. The x axis, showing years, spans from recruitment_start_year to recruitment_end_year, while the y axis, showing relative recruitment (R/R~0~), spans from rel_recruitment_min to rel_recruitment_max." -recruitment_deviations,figure,Annual deviations (on natural log scale) in the number of newly recruited fish the model estimates each year. ,"Scatterplot showing annual deviations in recruitment. Points have error bars and the dashed horizontal line at 0 represents no deviation from what would be estimated by the stock-recruit relationship. Positive values represent an increase in recruitment that year while negative values represent a decrease. The x axis, showing year, spans from recruit_dev_start_year to recruit_dev_end_year, while the y axis, showing the recruitment deviation, spans from recruit_dev_min to recruit_dev_max on a natural log scale." -tot_b,figure,Model-estimated biomass (B) time series. The horizontal dashed line represents the biomass limit reference point at biomass_ref_pt biomass_ref_pt_units.,"Line graph showing model-estimated biomass time series. The x axis, showing the year, spans from biomass_start_year to biomass_end_year, and the y axis, showing model-estimated biomass in biomass_units, spans from biomass_min to biomass_max." -spawning_biomass,figure,Model-estimated spawning stock biomass (SSB) time series. The horizontal dashed line represents the spawning stock biomass associated with the biomass limit reference point at ssb_ref_pt ssb_ref_pt_units.,"Line graph showing model-estimated spawning stock biomass. The x axis, showing the year, spans from ssb_start_year to ssb_end_year, and the y axis, showing model-estimated spawning stock biomass in ssb_units, spans from ssb_min to ssb_max." -relative_spawning_biomass,figure,"Model-estimated relative spawning stock biomass time series. The horizontal dashed line represents the limit reference point calculated as SSB/SSB(reference point), where SSB(reference point) is ssb_ref_pt ssb_ref_pt_units.","Line graph showing model-estimated relative spawning stock biomass. The x axis, showing the year, spans from ssb_start_year to ssb_end_year, and the y axis, showing model-estimated relative spawning stock biomass (SSB/SSB~target~), spans from rel_ssb_min to rel_ssb_max." -spr,figure,Model-estimated spawning potential ratio (SPR) (SSB~current~/SSB~target~) time series. The horizontal dashed line represents the spawning potential ratio of the limit reference point at spr_ref_pt spr_ref_pt_units.,"Line graph showing model-estimated spawning potential ratio over time. The x axis, showing the year, spans from spr_start_year to spr_end_year and the y axis, showing model-estimated spawning potential ratio in SSB~current~/SSB~target~, spans from spr_min to spr_max." -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." -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.", +kobe,figure,"Kobe plot showing stock status. Triangles delineate start and end years. Horizontal and vertical dashed lines delineate the proportion of F/F~MSY~ where F~MSY~ = B.ref.pt, and B/B~MSY~ where B~MSY~ = B.ref.pt. Overfishing is occurring when F/F~MSY~ > 1 and an overfished status is indicated where B/B~MSY~ > 1.","A Kobe plot showing stock status from kobe.start.year to kobe.end.year. The x axis, showing overfished status (i.e., B/B~MSY~), spans from B.BMSY.min to B.BMSY.max and the y axis, showing overfishing (i.e., F/F~MSY~), spans from F.FMSY.min to F.FMSY.max. The B/B~MSY~ and F/F~MSY~ for end.year.kobe were B.BMSY.end.yr and F.FMSY.end.yr, respectively, indicating that the stock overfished.status.is.isnot overfished and overfishing.status.is.is.not experiencing overfishing." +biomass,figure,Biomass (B) time series. The horizontal dashed line represents the limit reference point (B.ref.pt B.ref.pt.units).,"Line graph showing biomass time series. The x axis, showing the year, spans from B.start.year to B.end.year and the y axis, showing biomass in B.units, spans from B.min to B.max." +relative.biomass,figure,"Relative biomass (B) time series. The horizontal dashed line represents the limit reference point calculated as B/B(reference point), where B(reference point) is B.ref.point B.ref.pt.units.","Line graph showing relative biomass time series. The x axis, showing the year, spans from B.start.year to B.end.year and the y axis, showing relative biomass (B/B~target~), spans from rel.B.min to rel.B.max." +fishing.mortality,figure,Fishing mortality (F) over time. The horizontal dashed line represents the target reference point (F.ref.pt F.ref.pt.unit).,"Line graph showing fishing mortality over time . The x axis, showing the year, spans from F.start.year to F.end.year and the y axis, showing fishing mortality in F.units, spans from F.min to F.max." +landings,figure,Historical landings by fleet.,"Cumulative area plot showing historical landings. The x axis, showing the year, spans from landings.start.year to landings.end.year and the y axis, showing landings in landings.units, spans from landings.min to landings.max." +natural.mortality,figure,Natural mortality (M) for each age. ,"Line graph showing natural mortality. The x axis, showing age in M.units, spans from M.age.min to M.age.max and the y axis, showing the natural mortality rate per year, spans from M.rate.min to M.rate.max." +vonb.laa,figure,Aged and measured fish (points) and von Bertalanffy growth function (line) fit to the data.,"Point and line graph showing observations of measured age and length data as points and the von Bertalanffy relationship fit to this data as a line with 95% confidence intervals. The x axis, showing age in vonb.age.units, spans from vonb.age.min to vonb.age.max, and the y axis, showing length in vonb.length.units, spans from vonb.length.min to vonb.length.max." +length.type.conversion,figure,Length-type conversion relationship between total and fork length where points represent individual fish length measurement observations and the line is the fitted relationship.,"Point and line graph showing observations of measured fork length and measured total length from the same fish for conversion purposes as points, and a linear fit through those points as a line. The x axis, showing total length in total.length.units, spans from total.length.min to total.length.max and the y axis, showing fork length in fork.length.units, spans from fork.length.min to fork.length.max." +weight.length.converstion,figure,Weight-length conversion relationship where the points represent individual fish observations and the line is the fitted relationship. ,"Point and line graph showing observations of measured length and measured weight from the same fish for conversion purposes as points, and an exponential fit through those points as a line. The x axis, showing length in wl.length.units, spans from wl.length.min to wl.length.max, and the y axis, showing weight in wl.weight.units, spans from wl.weight.min to wl.weight.max." +maturity.schedule,figure,The relationship between the proportion mature and fish length. ,"Graph showing the relationship between fish maturity and length. Points, if present, show observations of maturity at different fish lengths and the line represents either the fit to the points, or the assumed or known maturity schedule. The x axis, showing length in prop.mat.length.units, spans from prop.mat.length.min to prop.mat.length.max and the y axis, showing the proportion mature, spans from 0--1." +fecundity.at.length,figure,Fecundity (in number of eggs) as a function of fish length. ,"Point and line graph showing observations of measured fecundity and measured length from the same fish and an exponential fit through those points displayed as a line. The x axis, showing length in fecundity.length.units, spans from fecundity.length.min to fecundity.length.max, and the y axis, showing fecundity in fecundity.units, spans from fecundity.min to fecundity.max." +CAA,figure,"Histograms showing the proportion of the catch in each age group for each year in which there is composition data, for fleet or survey fleet.or.survey.name.","Histograms for each year and fleet for which there is data (one per year grouped by fleet or survey), which show the proportion of the catch in each age group. The x axis of each histogram, showing age groups, span from caa.age.min to caa.age.max, while the y axis of each histogram, showing the proportion of the catch, spans from 0--1." +CAL,figure,"Histograms showing the proportion of the catch in each length group, each year for which there is composition data, for fleet or survey fleet.or.survey.name.","Histograms for each year and fleet for which there is data (one per year grouped by fleet or survey), which show the proportion of the catch in each length group. The x axis of each histogram contains length intervals that span from cal.length.min to cal.length.max, while the y axis of each histogram contains the proportion of the catch, which span from 0--1." +CPUE.indices,figure,Catch per unit effort (CPUE) over time for fleet or survey. 95% confidence intervals are shown for each survey/fleet.,"Line graph showing catch per unit effort (CPUE) over time for fleet or survey from cpue.start.year to cpue.end.year, stratified by survey/fleet. The x axis, showing the year, spans from cpue.start.year to cpue.end.year, and the y axis, showing CPUE in cpue.units, spans from cpue.min to cpue.max." +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." +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." +sr,figure,Stock recruitment relationship estimated by the assessment model. ,"Point and line graph showing the relationship between spawning stock biomass and newly recruited sr.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 sr.ssb.units, spans from sr.ssb.min to sr.ssb.max, while the y axis, showing recruitment in sr.units, spans from sr.min to sr.max." +recruitment,figure,Estimated recruitment by the assessment model each year in recruitment.units.,"Line graph showing the assessment model estimated recruitment in sr.units for each year. The x axis, showing years, spans from recruitment.start.year to recruitment.end.year, while the y axis, showing recruitment in recruitment.units, spans from recruitment.min to recruitment.max." +relative.recruitment,figure,"Estimated relative recruitment by the assessment model each year in recruitment.units, calculated as R/R~0~ where R~0~ is R0.","Line graph showing the assessment model estimated relative recruitment in sr.units for each year. The x axis, showing years, spans from recruitment.start.year to recruitment.end.year, while the y axis, showing relative recruitment (R/R~0~), spans from rel.recruitment.min to rel.recruitment.max." +recruitment.deviations,figure,Annual deviations (on natural log scale) in the number of newly recruited fish the model estimates each year. ,"Scatterplot showing annual deviations in recruitment. Points have error bars and the dashed horizontal line at 0 represents no deviation from what would be estimated by the stock-recruit relationship. Positive values represent an increase in recruitment that year while negative values represent a decrease. The x axis, showing year, spans from recruit.dev.start.year to recruit.dev.end.year, while the y axis, showing the recruitment deviation, spans from recruit.dev.min to recruit.dev.max on a natural log scale." +tot.b,figure,Model-estimated biomass (B) time series. The horizontal dashed line represents the biomass limit reference point at biomass.ref.pt biomass.ref.pt.units.,"Line graph showing model-estimated biomass time series. The x axis, showing the year, spans from biomass.start.year to biomass.end.year, and the y axis, showing model-estimated biomass in biomass.units, spans from biomass.min to biomass.max." +spawning.biomass,figure,Model-estimated spawning stock biomass (SSB) time series. The horizontal dashed line represents the spawning stock biomass associated with the biomass limit reference point at ssb.ref.pt ssb.ref.pt.units.,"Line graph showing model-estimated spawning stock biomass. The x axis, showing the year, spans from ssb.start.year to ssb.end.year, and the y axis, showing model-estimated spawning stock biomass in ssb.units, spans from ssb.min to ssb.max." +relative.spawning.biomass,figure,"Model-estimated relative spawning stock biomass time series. The horizontal dashed line represents the limit reference point calculated as SSB/SSB(reference point), where SSB(reference point) is ssb.ref.pt ssb.ref.pt.units.","Line graph showing model-estimated relative spawning stock biomass. The x axis, showing the year, spans from ssb.start.year to ssb.end.year, and the y axis, showing model-estimated relative spawning stock biomass (SSB/SSB~target~), spans from rel.ssb.min to rel.ssb.max." +spr,figure,Model-estimated spawning potential ratio (SPR) (SSB~current~/SSB~target~) time series. The horizontal dashed line represents the spawning potential ratio of the limit reference point at spr.ref.pt spr.ref.pt.units.,"Line graph showing model-estimated spawning potential ratio over time. The x axis, showing the year, spans from spr.start.year to spr.end.year and the y axis, showing model-estimated spawning potential ratio in SSB~current~/SSB~target~, spans from spr.min to spr.max." +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." +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.", +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.",