In iantaylor-NOAA/Lingcod_2021: Estimate the Status of Lingcod off the US West Coast in 2021

\clearpage \floatplacement{table}{H}

Tables

sa4ss::read_child(string_switchletter(
  file.path("..", "tables", "table-catchbystate-s-.tex"),
  params$area
))

management_oflabcacl <- utils::read.csv(file.path("..", "tables", "management-oflabcacl.csv"))
management_oflabcacl %>%
  dplyr::filter(area == params$area) %>%
  dplyr::select(-area) %>%
  dplyr::left_join(
    x = .,
    y = model[["catch"]] %>%
      dplyr::group_by(Yr) %>%
      dplyr::summarize(Observed = sum(Obs, na.rm = TRUE), Expected = sum(kill_bio, na.rm = TRUE), .groups = "keep") %>%
      dplyr::ungroup(),
    by = c(Year = "Yr")
  ) %>%
  dplyr::mutate_at(2:NCOL(.), ~ sprintf("%.2f", .x)) %>%
  kableExtra::kbl(
    longtable = FALSE, booktabs = TRUE, format = "latex",
    caption = paste0(
      "Recent trends in observed landings and expected dead biomass (mt) relative to management guidelines (\\glsentrylong{ofl}, \\glsentryshort{ofl}; \\glsentrylong{abc}, \\glsentryshort{abc}; \\glsentrylong{acl}, \\glsentryshort{acl}). Expected dead biomass represents the total landings plus the model-estimated dead discard biomass.",
      " ", text_wcgop, " ",
      "Additionally, management in 2011 and 2012 was based on a break at 42\\textdegree00\\textquotesingle N versus all other years used \\CapeM."
    ),
    label = "management-refpoints"
  ) %>%
  kableExtra::add_header_above(c(" ", "Management" = 3, "Landings" = 2)) %>%
  kableExtra::kable_styling(latex_options = c("repeat_header"))

ignore <- mapply(sa4ss::read_child, "../tables/cpue-commercialfixed-gear-filter.tex")
ignore <- mapply(sa4ss::read_child, "../tables/reccpuewa-filtersummary.tex")
ignore <- mapply(sa4ss::read_child, "../tables/cpue-recreationalOregon-filter.tex")
ignore <- mapply(sa4ss::read_child, "../tables/cpue-recreationalCaliforniaN-filter.tex")

```{asis, opts.label="south"} \begin{table}

\caption{\label{tab:data-filter-cpfvonboard}Data filtering for the California \glsentrylong{cpfv} onboard survey of lingcod in the southern California recreational fishery.} \centering \begin{tabular}[t]{>{\raggedright\arraybackslash}p{10em}>{\raggedright\arraybackslash}p{15em}c>{\centering\arraybackslash}p{5em}>{\centering\arraybackslash}p{5em}} \toprule Filter & Description & Trip & Positive Trips & \% drifts retained\ \midrule \cellcolor{gray!6}{All} & \cellcolor{gray!6}{Download from SQL; identifiable errors filtered} & \cellcolor{gray!6}{41168} & \cellcolor{gray!6}{1866} & \cellcolor{gray!6}{5\%}\ Fishery closed & Removed samples when target fish fishery closed & 33224 & 1834 & 6\%\ \cellcolor{gray!6}{Ocean only} & \cellcolor{gray!6}{Removed samples from major bays} & \cellcolor{gray!6}{33029} & \cellcolor{gray!6}{1834} & \cellcolor{gray!6}{6\%}\ Catch & Removed samples with zero catch of any species & 30469 & 1834 & 6\%\ \cellcolor{gray!6}{Depth} & \cellcolor{gray!6}{Removed samples in less than max depth of species} & \cellcolor{gray!6}{29858} & \cellcolor{gray!6}{1817} & \cellcolor{gray!6}{6\%}\ \addlinespace Time fished & Removed upper two percent of time fished & 29252 & 1802 & 6\%\ \cellcolor{gray!6}{Percent groundfish in samples} & \cellcolor{gray!6}{Removed samples with fewer groundfish than when the target observed} & \cellcolor{gray!6}{14664} & \cellcolor{gray!6}{1718} & \cellcolor{gray!6}{12\%}\ Another area gfish filter & Removed samples & 9043 & 1469 & 16\%\ \bottomrule \end{tabular} \end{table}

<!-- Unused fishery-dependent data -->
```r
ignore <- mapply(sa4ss::read_child, "../tables/fi-index-ormarres-N.tex")
ignore <- mapply(sa4ss::read_child, "../tables/fi-index-ormarres-mr.tex")

```{asis, opts.label = "south"} \begin{table} \caption{\label{tab:tab-depth-nwfschl}Positive samples of lingcod in the \glsentrylong{s-hkl} by depth (fm).} \centering \begin{tabular}[t]{lrrl} \toprule Year & Positive Samples & Samples & Percent Positive\ \midrule \cellcolor{gray!6}{(0,50]} & \cellcolor{gray!6}{4} & \cellcolor{gray!6}{207} & \cellcolor{gray!6}{2\%}\ (50,75] & 86 & 724 & 12\%\ \cellcolor{gray!6}{(75,100]} & \cellcolor{gray!6}{226} & \cellcolor{gray!6}{2383} & \cellcolor{gray!6}{9\%}\ (100,125] & 123 & 1620 & 8\%\ \cellcolor{gray!6}{(125,150]} & \cellcolor{gray!6}{101} & \cellcolor{gray!6}{1121} & \cellcolor{gray!6}{9\%}\ \addlinespace (150,175] & 98 & 982 & 10\%\ \cellcolor{gray!6}{(175,200]} & \cellcolor{gray!6}{20} & \cellcolor{gray!6}{268} & \cellcolor{gray!6}{7\%}\ (200,230] & 14 & 97 & 14\%\ \bottomrule \end{tabular} \end{table}

\begin{table} \caption{\label{tab:tab-depthsite-nwfschl}Samples of lingcod in the \glsentrylong{s-hkl} by area and depth bins (ft).} \centering \resizebox{\linewidth}{!}{ \begin{tabular}[t]{lllllllll} \toprule Area name & (125,150] & (175,200] & (200,230] & (0,50] & (50,75] & (75,100] & (100,125] & (150,175]\ \midrule \cellcolor{gray!6}{Fourteen Mile Bank} & \cellcolor{gray!6}{1\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{}\ 107 and 118 Banks & & 5\% & 0\% & & & & & \ \cellcolor{gray!6}{43 Fathom Bank} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{3\%} & \cellcolor{gray!6}{10\%} & \cellcolor{gray!6}{}\ Anacapa Island & 18\% & 0\% & & & 0\% & 4\% & 4\% & 9\%\ \cellcolor{gray!6}{Catalina Island} & \cellcolor{gray!6}{10\%} & \cellcolor{gray!6}{11\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{1\%} & \cellcolor{gray!6}{1\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{11\%}\ \addlinespace Central Coast & & & & & & 2\% & 0\% & \ \cellcolor{gray!6}{Cherry Bank} & \cellcolor{gray!6}{10\%} & \cellcolor{gray!6}{5\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{9\%} & \cellcolor{gray!6}{10\%} & \cellcolor{gray!6}{}\ Cortez Bank & 4\% & & & 12\% & 6\% & 5\% & 3\% & 7\%\ \cellcolor{gray!6}{Garrett Bank} & \cellcolor{gray!6}{6\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{}\ Harrison Reef & 0\% & & & & & 2\% & 1\% & \ \addlinespace \cellcolor{gray!6}{Hidden Reef} & \cellcolor{gray!6}{25\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{7\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{9\%}\ Kidney Bank & 11\% & & & & & & 12\% & 0\%\ \cellcolor{gray!6}{Nine Mile Bank} & \cellcolor{gray!6}{1\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{0\%}\ Osborn Bank & & & & 0\% & 15\% & 32\% & & 24\%\ \cellcolor{gray!6}{Point Conception/Arguello} & \cellcolor{gray!6}{14\%} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{11\%} & \cellcolor{gray!6}{11\%} & \cellcolor{gray!6}{3\%}\ \addlinespace Potato Bank & 4\% & & & & & 20\% & 8\% & \ \cellcolor{gray!6}{San Clemente Island} & \cellcolor{gray!6}{8\%} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{1\%} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{6\%} & \cellcolor{gray!6}{1\%} & \cellcolor{gray!6}{5\%}\ San Miguel Island & 10\% & & & & 41\% & 22\% & 10\% & \ \cellcolor{gray!6}{San Nicolas Island East} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{17\%} & \cellcolor{gray!6}{25\%} & \cellcolor{gray!6}{33\%} & \cellcolor{gray!6}{5\%}\ San Nicolas Island West & 40\% & 0\% & & & 5\% & 11\% & 20\% & 5\%\ \addlinespace \cellcolor{gray!6}{San Pedro Bay} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{4\%} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{}\ Santa Barbara & & & & 1\% & 17\% & 5\% & & \ \cellcolor{gray!6}{Santa Barbara Channel} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{2\%} & \cellcolor{gray!6}{13\%}\ Santa Barbara Island & 8\% & 8\% & 0\% & 4\% & 0\% & 12\% & 15\% & 19\%\ \cellcolor{gray!6}{Santa Cruz Island} & \cellcolor{gray!6}{33\%} & \cellcolor{gray!6}{15\%} & \cellcolor{gray!6}{20\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{6\%} & \cellcolor{gray!6}{9\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{17\%}\ \addlinespace Santa Monica Bay & 1\% & & & & & 1\% & 0\% & \ \cellcolor{gray!6}{Santa Rosa Flats} & \cellcolor{gray!6}{11\%} & \cellcolor{gray!6}{6\%} & \cellcolor{gray!6}{15\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{9\%} & \cellcolor{gray!6}{11\%}\ Santa Rosa Island & & & & & 18\% & 19\% & 0\% & \ \cellcolor{gray!6}{Sixty Mile Bank} & \cellcolor{gray!6}{2\%} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{2\%} & \cellcolor{gray!6}{0\%}\ South Coast & & & & 0\% & 3\% & 6\% & & \ \addlinespace \cellcolor{gray!6}{Tanner Bank} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{7\%} & \cellcolor{gray!6}{0\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{3\%} & \cellcolor{gray!6}{} & \cellcolor{gray!6}{0\%}\ \bottomrule \end{tabular}} \end{table}

\begin{table} \caption{\label{tab:tab-year-nwfschl}Samples of lingcod in the \glsentrylong{s-hkl} by year.} \centering \begin{tabular}[t]{lrrl} \toprule Year & Positive Samples & Samples & Percent Positive\ \midrule \cellcolor{gray!6}{2004} & \cellcolor{gray!6}{29} & \cellcolor{gray!6}{270} & \cellcolor{gray!6}{11\%}\ 2005 & 27 & 307 & 9\%\ \cellcolor{gray!6}{2006} & \cellcolor{gray!6}{17} & \cellcolor{gray!6}{303} & \cellcolor{gray!6}{6\%}\ 2007 & 27 & 335 & 8\%\ \cellcolor{gray!6}{2008} & \cellcolor{gray!6}{11} & \cellcolor{gray!6}{412} & \cellcolor{gray!6}{3\%}\ \addlinespace 2009 & 16 & 405 & 4\%\ \cellcolor{gray!6}{2010} & \cellcolor{gray!6}{11} & \cellcolor{gray!6}{414} & \cellcolor{gray!6}{3\%}\ 2011 & 30 & 393 & 8\%\ \cellcolor{gray!6}{2012} & \cellcolor{gray!6}{53} & \cellcolor{gray!6}{414} & \cellcolor{gray!6}{13\%}\ 2013 & 62 & 409 & 15\%\ \addlinespace \cellcolor{gray!6}{2014} & \cellcolor{gray!6}{67} & \cellcolor{gray!6}{530} & \cellcolor{gray!6}{13\%}\ 2015 & 75 & 615 & 12\%\ \cellcolor{gray!6}{2016} & \cellcolor{gray!6}{77} & \cellcolor{gray!6}{623} & \cellcolor{gray!6}{12\%}\ 2017 & 69 & 652 & 11\%\ \cellcolor{gray!6}{2018} & \cellcolor{gray!6}{64} & \cellcolor{gray!6}{660} & \cellcolor{gray!6}{10\%}\ \addlinespace 2019 & 37 & 660 & 6\%\ \bottomrule \end{tabular} \end{table}

<!-- Sample size tables -->
```r

sa4ss::read_child(filein = file.path("..", "tables", paste0("length_samps_", params$area, ".tex")))

sa4ss::read_child(filein = file.path("..", "tables", paste0("age_samps_", params$area, ".tex")))

sa4ss::read_child(filein = file.path("..", "tables", paste0("length_samps_comm_byState_", params$area, ".tex")))

sa4ss::read_child(filein = file.path("..", "tables", paste0("age_samps_comm_byState_", params$area, ".tex")))

\begin{table} \caption{(#tab:tab-region-ccfrp)\glsfirst{s-ccfrp} samples of r spp by subregion used to generate an index of abundance.} \centering \begin{tabular}[t]{lrrr} \toprule Year & Samples & Positive Samples & \% Positive\ \midrule \cellcolor{gray!6}{South Cape Mendocino} & \cellcolor{gray!6}{131} & \cellcolor{gray!6}{289} & \cellcolor{gray!6}{45\%}\ Ten Mile & 139 & 297 & 47\%\ \cellcolor{gray!6}{Stewarts Point} & \cellcolor{gray!6}{127} & \cellcolor{gray!6}{293} & \cellcolor{gray!6}{43\%}\ Bodega Head & 139 & 275 & 51\%\ \cellcolor{gray!6}{Ano Nuevo} & \cellcolor{gray!6}{701} & \cellcolor{gray!6}{1879} & \cellcolor{gray!6}{37\%}\ \addlinespace Point Lobos & 553 & 1369 & 40\%\ \cellcolor{gray!6}{Piedras Blancas} & \cellcolor{gray!6}{384} & \cellcolor{gray!6}{953} & \cellcolor{gray!6}{40\%}\ Point Buchon & 535 & 1324 & 40\%\ \cellcolor{gray!6}{Anacapa Island} & \cellcolor{gray!6}{3} & \cellcolor{gray!6}{52} & \cellcolor{gray!6}{6\%}\ Carrington Point & 93 & 182 & 51\%\ \addlinespace \cellcolor{gray!6}{South La Jolla} & \cellcolor{gray!6}{9} & \cellcolor{gray!6}{50} & \cellcolor{gray!6}{18\%}\ \bottomrule \end{tabular} \end{table}

``{asis, opts.label = 'south', echo = TRUE} \begin{table} \caption{(\#tab:tab-year-ccfrp)Samples ofr spp` in the \glsfirst{s-ccfrp} data by year.} \centering \begin{tabular}[t]{lrrr} \toprule Year & Samples & Positive Samples & \% Positive\ \midrule \cellcolor{gray!6}{2007} & \cellcolor{gray!6}{87} & \cellcolor{gray!6}{552} & \cellcolor{gray!6}{16\%}\ 2008 & 134 & 564 & 24\%\ \cellcolor{gray!6}{2009} & \cellcolor{gray!6}{94} & \cellcolor{gray!6}{370} & \cellcolor{gray!6}{25\%}\ 2010 & 142 & 420 & 34\%\ \cellcolor{gray!6}{2011} & \cellcolor{gray!6}{170} & \cellcolor{gray!6}{374} & \cellcolor{gray!6}{45\%}\ \addlinespace 2012 & 237 & 397 & 60\%\ \cellcolor{gray!6}{2013} & \cellcolor{gray!6}{201} & \cellcolor{gray!6}{428} & \cellcolor{gray!6}{47\%}\ 2014 & 262 & 449 & 58\%\ \cellcolor{gray!6}{2015} & \cellcolor{gray!6}{135} & \cellcolor{gray!6}{224} & \cellcolor{gray!6}{60\%}\ 2016 & 240 & 429 & 56\%\ \addlinespace \cellcolor{gray!6}{2017} & \cellcolor{gray!6}{304} & \cellcolor{gray!6}{590} & \cellcolor{gray!6}{52\%}\ 2018 & 332 & 700 & 47\%\ \cellcolor{gray!6}{2019} & \cellcolor{gray!6}{279} & \cellcolor{gray!6}{740} & \cellcolor{gray!6}{38\%}\ 2020 & 197 & 726 & 27\%\ \bottomrule \end{tabular} \end{table}

\begin{table} \caption{(#tab:tab-depth-ccfrp)Positive samples of r spp in the \glsfirst{s-ccfrp} data by depth (fm) bin.} \centering \begin{tabular}[t]{lrrr} \toprule Year & Samples & Positive Samples & \% Positive\ \midrule \cellcolor{gray!6}{(0,10]} & \cellcolor{gray!6}{589} & \cellcolor{gray!6}{1809} & \cellcolor{gray!6}{33\%}\ (10,15] & 1215 & 2942 & 41\%\ \cellcolor{gray!6}{(15,20]} & \cellcolor{gray!6}{834} & \cellcolor{gray!6}{1827} & \cellcolor{gray!6}{46\%}\ (20,30] & 176 & 385 & 46\%\ \bottomrule \end{tabular} \end{table}

\begin{table} \caption{(#tab:tab-model-select-ccfrp)Model selection for the \glsfirst{s-ccfrp} index was performed using \glsfirst{aic} to select factors that explained the data in the most parsimonious manner.} \centering \begin{tabular}[t]{lrr} \toprule Model & Binomial $\Delta$AIC & Lognormal $\Delta$AIC\ \midrule \cellcolor{gray!6}{1} & \cellcolor{gray!6}{873.41} & \cellcolor{gray!6}{775.69}\ YEAR + AREA & 237.89 & 160.63\ \cellcolor{gray!6}{YEAR + AREA + SITE} & \cellcolor{gray!6}{55.57} & \cellcolor{gray!6}{46.76}\ YEAR + AREA + SITE + DEPTH bin & 0.00 & 0.00\ \cellcolor{gray!6}{YEAR + SITE + DEPTH bin} & \cellcolor{gray!6}{83.23} & \cellcolor{gray!6}{403.90}\ \addlinespace YEAR + DEPTH bin & 241.15 & 497.94\ \cellcolor{gray!6}{YEAR + AREA + DEPTH bin} & \cellcolor{gray!6}{151.37} & \cellcolor{gray!6}{97.41}\ \bottomrule \end{tabular} \end{table}

\begin{table} \caption{(#tab:tab-index-ccfrp)Standardized index for the \glsfirst{s-ccfrp} survey index with log-scale standard errors (SE) and 95\% highest posterior density (HPD) intervals for r spp.} \centering \begin{tabular}[t]{rrrrr} \toprule Year & Mean & log SE & lower HPD & upper HPD\ \midrule \cellcolor{gray!6}{2007} & \cellcolor{gray!6}{0.24} & \cellcolor{gray!6}{0.19} & \cellcolor{gray!6}{0.16} & \cellcolor{gray!6}{0.33}\ 2008 & 0.30 & 0.16 & 0.21 & 0.40\ \cellcolor{gray!6}{2009} & \cellcolor{gray!6}{0.35} & \cellcolor{gray!6}{0.17} & \cellcolor{gray!6}{0.25} & \cellcolor{gray!6}{0.49}\ 2010 & 0.45 & 0.14 & 0.33 & 0.58\ \cellcolor{gray!6}{2011} & \cellcolor{gray!6}{0.63} & \cellcolor{gray!6}{0.13} & \cellcolor{gray!6}{0.49} & \cellcolor{gray!6}{0.79}\ \addlinespace 2012 & 0.85 & 0.10 & 0.69 & 1.03\ \cellcolor{gray!6}{2013} & \cellcolor{gray!6}{0.77} & \cellcolor{gray!6}{0.12} & \cellcolor{gray!6}{0.60} & \cellcolor{gray!6}{0.97}\ 2014 & 1.08 & 0.10 & 0.87 & 1.30\ \cellcolor{gray!6}{2015} & \cellcolor{gray!6}{1.19} & \cellcolor{gray!6}{0.11} & \cellcolor{gray!6}{0.94} & \cellcolor{gray!6}{1.46}\ 2016 & 0.92 & 0.11 & 0.74 & 1.13\ \addlinespace \cellcolor{gray!6}{2017} & \cellcolor{gray!6}{0.78} & \cellcolor{gray!6}{0.10} & \cellcolor{gray!6}{0.63} & \cellcolor{gray!6}{0.95}\ 2018 & 0.56 & 0.11 & 0.44 & 0.68\ \cellcolor{gray!6}{2019} & \cellcolor{gray!6}{0.38} & \cellcolor{gray!6}{0.13} & \cellcolor{gray!6}{0.29} & \cellcolor{gray!6}{0.49}\ 2020 & 0.43 & 0.15 & 0.31 & 0.56\ \bottomrule \end{tabular} \end{table}

<!-- ====================================================================== -->
<!-- 30model tables -->
<!-- ====================================================================== -->
```r
table_outputconfig(model)
cat("\\begin{landscape}")
table_pars(model)
cat("\\end{landscape}")
table_likelihoods(model)
table_dq(model)
table_ts(model)
table_compweight(model)

\begin{landscape}

table_sens(string_switchletter("../tables/sens_table_s_bio_rec.csv", params$area),
           sens_group = "biology and recruitment")
table_sens(string_switchletter("../tables/sens_table_s_comp.csv", params$area),
           sens_group = "composition data")
table_sens(string_switchletter("../tables/sens_table_s_index.csv", params$area),
           sens_group = "indices",
           caption_extra = "The first sensitivity is an alternative recreational index. Other column names refer to index data that were taken out of the model.")
table_sens(string_switchletter("../tables/sens_table_s_sel.csv", params$area),
           sens_group = "selectivity")

\end{landscape}

sa4ss::read_child(file.path(
  paste0(
    params$model,
    "_profile_NatM_uniform_Fem_GP_1_prior_like_1"
  ),
  "profile-M.tex"
))

sa4ss::read_child(file.path(paste0(params$model, "_retro"), "mohnsrho.tex"))

\begin{landscape}

table_sens("../tables/table_compare_north_vs_south.csv",
           caption = "Comparison of estimates of key parameters and derived quantities between the base model for north and south and the 2017 assessments for north and south. Note that the boundary between north and south differs between the current and 2017 assessments.")

\end{landscape}

ignore <- table_projections(model)
cat(ignore)

decisiontable <- append(
  x = readLines(file.path("..", mod_loc, "decision_table.tex")),
  values = c("\\caption{\\label{tab:decision}Decision table with 10-year projections based on two years of recent average catch, alternative states of nature (columns), and management assumptions (rows) annual catch limits (ACLs) defined using an estimate of uncertainty (i.e., $P^*$) of 0.40 and 0.45. Colors of catch and fraction unfished are relative with lighter colors representing lower values. Italics indicate years were the full catch could not be removed from the low state of nature because of insufficient biomass.}"),
  after = 1
)
cat(decisiontable)

iantaylor-NOAA/Lingcod_2021 documentation built on Oct. 30, 2024, 6:42 p.m.