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Updated broken table
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jimianelli committed Nov 16, 2024
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16 changes: 8 additions & 8 deletions _quarto.yml
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Expand Up @@ -80,14 +80,14 @@ format:
#number-sections: false
header-includes:
- \counterwithout{figure}{chapter}
- \usepackage{fancyhdr}
- \pagestyle{fancy}
- \fancyhf{}
- \lhead{September}
- \rhead{2024}
- \chead{--Draft--}
- \rfoot{\thepage}
- \lfoot{EBS pollock assessment discussion paper }
# - \usepackage{fancyhdr}
# - \pagestyle{fancy}
# - \fancyhf{}
# - \lhead{September}
# - \rhead{2024}
# - \chead{--Draft--}
# - \rfoot{\thepage}
# - \lfoot{EBS pollock assessment discussion paper }

epub:
metadata:
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22 changes: 12 additions & 10 deletions doc/vast.qmd
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Expand Up @@ -18,16 +18,18 @@ explanation of settings.

The software versions of dependent programs used to generate VAST estimates were:

* R (4.3.0)
* MKL libraries via Microsoft R Open (4.0.2)
* INLA (21.11.22)
* Matrix (1.4-0)
* TMB (1.9.6)
* TMBhelper (1.4.0)
* VAST (3.10.1)
* FishStatsUtils (2.12.1)

For these model-based index time series, we used the same VAST model run settings.
* R (4.3.0)
* MKL libraries via Microsoft R Open (4.0.2)
* INLA (23.09.09)
* Matrix (1.6-1.1)
* TMB (1.9.6)
* TMBhelper (1.4.0)
* VAST (3.10.1)
* FishStatsUtils (2.12.1)


For EBS pollock we used data on biomass per unit area from all grid cells (and corner stations for 1982-2023) in the 83-112 bottom trawl survey of the EBS, 1982-2024, including exploratory northern extension samples in 2001, 2005, and 2006, as well as 83-112 samples available in the NBS in 1982, 1985, 1988, 1991, 2010, and 2017-2023 (except 2020). NBS samples collected prior to 2010 and in 2018 did not follow the 20 nautical mile sampling grid used in the 2010, 2017, 2019, and 2021-2023 surveys. Assimilating these data therefore required extrapolating into unsampled areas. As before, we included a a spatially varying covariate of the cold-pool extent (Thorson 2019, O’Leary et al. 2020). All environmental data used as covariates were computed within the R package coldpool (Rohan et al., 2022).


## Spatio-temporal treatment of survey data on pollock density

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156 changes: 79 additions & 77 deletions ebswp.qmd
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@@ -1,6 +1,6 @@
---
title: "1. Assessment of walleye pollock in the eastern Bering Sea"
subtitle: "Draft for November 2024 Plan Team review"
subtitle: "Draft for December 2024 Council review"
author:
- name: James Ianelli
corresponding: true
Expand Down Expand Up @@ -48,16 +48,17 @@ format:
keep-tex: true
extra_dependencies: rotating
header-includes:
- \usepackage{fancyhdr}
# - \usepackage{fancyhdr}
- \pagenumbering{gobble}
# - \pagestyle{fancy}
- \fancyhf{}
- \lhead{\textit{November 2024 Plan Team}}
- \rhead{\textit{EBS pollock }}
- \chead{\textit{--Draft--}}
- \cfoot{\textit{\thepage}}
- \rfoot{}
- \lfoot{}
- \setlength{\footskip}{4cm} # Lower the footer
# - \fancyhf{}
# - \lhead{\textit{November 2024 Plan Team}}
# - \rhead{\textit{EBS pollock }}
# - \chead{\textit{--Draft--}}
# - \cfoot{\textit{\thepage}}
# - \rfoot{}
# - \lfoot{}
# - \setlength{\footskip}{4cm} # Lower the footer
editor_options:
chunk_output_type: console
editor:
Expand All @@ -82,11 +83,11 @@ date: 11/15/2024
\vspace{2.0in}
<!-- \medskip % or \bigskip for larger spacing -->

<div style="margin-bottom: 4.5in;"></div>
*This information is distributed solely for the purpose of pre-dissemination
peer review under applicable information quality guidelines. It has not been
formally disseminated by the National Marine Fisheries Service and should not
be construed to represent any agency determination or policy.*
<!-- <div style="margin-bottom: 4.5in;"></div> -->
<!-- *This information is distributed solely for the purpose of pre-dissemination -->
<!-- peer review under applicable information quality guidelines. It has not been -->
<!-- formally disseminated by the National Marine Fisheries Service and should not -->
<!-- be construed to represent any agency determination or policy.* -->


```{r setup}
Expand Down Expand Up @@ -242,8 +243,8 @@ less prior influence) assumptions about the stock-recruitment relationship were
Tier & 1a & 1a & `r M$tier3ab1 ` & `r M$tier3ab2 ` \\
Projected total (age 3+) biomass (t) & `r M$it$a1[1]` t & `r M$it$a2[1]` t & `r M$age3plus1s` t & `r M$age3plus2s` t \\
Projected female spawning biomass (t) & `r M$it$b1[1]` t & `r M$it$b2[1]` t & `r M$ssb1s` t & `r M$ssb2s` t \\
$B_0$ & `r M$it$c1[1]` t & `r M$it$c2[1]` t & `r M$b100s`,000 t & `r M$b100s`,000 t \\
$B_{msy}$ & `r M$it$d1[1]` t & `r M$it$d2[1]` t & `r M$b35s`,000 t & `r M$b35s`,000 t \\
$B_0(B_{100\%})$ & `r M$it$c1[1]` t & `r M$it$c2[1]` t & `r M$b100s`,000 t & `r M$b100s`,000 t \\
$B_{msy}(B_{35\%})$ & `r M$it$d1[1]` t & `r M$it$d2[1]` t & `r M$b35s`,000 t & `r M$b35s`,000 t \\
$F_{OFL}$ & `r M$it[1,8]` & `r M$it[2,8]` & `r round(M$Tier3_FOFL1,3)` & `r round(M$Tier3_FOFL2,3) ` \\
$maxF_{ ABC}$ & `r M$it[1,9]` & `r M$it[2,9]` & `r round(M$Tier3_FABC1,3) ` & `r round(M$Tier3_FABC2,3) ` \\
$F_{ABC}$ & `r M$it[1,10]`& `r M$it[2,10]`& `r round(M$Tier3_FABC1,3)` & `r round(M$Tier3_FABC2,3)` \\
Expand Down Expand Up @@ -3282,9 +3283,9 @@ Year & E & W & US & RU & E & W & US & RU & E &
2012 & 17 & 60 & 77 & 14 & 4,422 & 23,929 & 28,351 & 5,620 & 650 & 2,045 & 2,695 & 418 & 646 & 1,483 & 2,129 & 416 \\
2014 & 52 & 87 & 139 & 3 & 28,857 & 8,645 & 37,502 & 747 & 1,739 & 849 & 2,588 & 72 & 845 & 1,735 & 2,580 & 72 \\
2016 & 37 & 71 & 108 & & 10,912 & 24,134 & 35,046 & & 880 & 1,514 & 2,394 & & 876 & 1,513 & 2,388 & \\
2018 & 36 & 64 & 100 & & 11,031 & 21,173 & 32,204 & & 1,105 & 1,750 & 2,855 & & 1,100 & 1,743 & 2,843 & \\
2022 & 26 & 36 & 62 & & 4,954 & 11,994 & 16,948 & & 671 & 1,691 & 2,362 & & 668 & 1,688 & 2,356 & \\
2024 & 13 & 41 & 55 & & 4,954 & 11,994 & 16,948 & & 671 & 1,691 & 2,362 & & 668 & 1,688 & 2,356 & \\
2018 & 36 & 64 & 100 & & 11,031 & 21,173 & 32,204 & & 1,105 & 1,750 & 2,855 & & 1,100 & 1,743 & 2,843 & \\
2022 & 26 & 36 & 62 & & 4,954 & 11,994 & 16,948 & & 671 & 1,691 & 2,362 & & 668 & 1,688 & 2,356 & \\
2024 & 14 & 41 & 55 & & 4,535 & 14,472 & 19,007 & & 725 & 1,561 & 2,286 & & & & & \\
\hline
\end{tabular}
}
Expand Down Expand Up @@ -3656,7 +3657,7 @@ for (i in seq(2, length(t3[1, ]), 2)) {
}
#
#tab <- xtable(t3, caption = cap, label = "tbl:biom3plus", digits = 0, auto = TRUE, align = rep("r", (length(t3[1, ]) + 1)))
knitr::kable(tab, align='r', caption=cap)
knitr::kable(t3, align='r', caption=cap)
#
# #cat("\\resizebox{\\textwidth}{!}{%")
#print(tab, caption.placement = "top", tabular.environment = "longtable",
Expand Down Expand Up @@ -3832,7 +3833,7 @@ print(tab, caption.placement = "top", include.rownames = FALSE, sanitize.text.fu
# 41,tier3_ABC,"Tier 3 projections of EBS pollock ABC (given catches in Table \ref{tbl:tier3_C}) for the 7 scenarios.
# 42,tier3_F,"Tier 3 projections of EBS pollock fishing mortality for the 7 scenarios.
# 43,tier3_SSB,"Tier 3 projections of EBS pollock spawning biomass (kt) for the 7 scenarios. Note that the values for B100\%, B40\%, and B35\% are `r b100s`, `r b40s`, `r b35s`, thousand t, respectively."
# print_Tier3_tbl(thismod)
print_Tier3_tbl(thismod)
# print_Tier3_tables(3)
```
\begin{table}[ht]
Expand All @@ -3844,19 +3845,19 @@ print(tab, caption.placement = "top", include.rownames = FALSE, sanitize.text.fu
Catch & Scenario.1 & Scenario.2 & Scenario.3 & Scenario.4 & Scenario.5 & Scenario.6 & Scenario.7 \\
\hline
2025 & 1,350 & 1,350 & 1,350 & 1,350 & 1,350 & 1,350 & 1,350 \\
2026 & 1,350 & 1,350 & 1,350 & 1,350 & 1,350 & 2,377 & 1,964 \\
2027 & 1,793 & 1,793 & 1,123 & 812 & 0 & 1,648 & 1,556 \\
2028 & 1,614 & 1,614 & 1,120 & 846 & 0 & 1,609 & 1,825 \\
2029 & 1,604 & 1,604 & 1,214 & 943 & 0 & 1,682 & 1,761 \\
2030 & 1,570 & 1,570 & 1,247 & 992 & 0 & 1,669 & 1,697 \\
2031 & 1,591 & 1,591 & 1,292 & 1,046 & 0 & 1,696 & 1,704 \\
2032 & 1,598 & 1,598 & 1,318 & 1,083 & 0 & 1,700 & 1,702 \\
2033 & 1,587 & 1,587 & 1,320 & 1,094 & 0 & 1,682 & 1,682 \\
2034 & 1,581 & 1,581 & 1,323 & 1,103 & 0 & 1,674 & 1,674 \\
2035 & 1,567 & 1,567 & 1,314 & 1,101 & 0 & 1,658 & 1,658 \\
2036 & 1,560 & 1,560 & 1,311 & 1,102 & 0 & 1,649 & 1,649 \\
2037 & 1,555 & 1,555 & 1,308 & 1,100 & 0 & 1,646 & 1,646 \\
2038 & 1,551 & 1,551 & 1,303 & 1,097 & 0 & 1,643 & 1,643 \\
2026 & 1,350 & 1,350 & 1,350 & 1,350 & 1,350 & 2,495 & 2,035 \\
2027 & 1,801 & 1,801 & 1,062 & 786 & 0 & 1,578 & 1,503 \\
2028 & 1,594 & 1,594 & 1,067 & 825 & 0 & 1,582 & 1,820 \\
2029 & 1,589 & 1,589 & 1,163 & 922 & 0 & 1,679 & 1,758 \\
2030 & 1,613 & 1,613 & 1,246 & 1,009 & 0 & 1,728 & 1,753 \\
2031 & 1,627 & 1,627 & 1,295 & 1,069 & 0 & 1,736 & 1,742 \\
2032 & 1,616 & 1,616 & 1,309 & 1,095 & 0 & 1,721 & 1,722 \\
2033 & 1,607 & 1,607 & 1,312 & 1,106 & 0 & 1,706 & 1,706 \\
2034 & 1,603 & 1,603 & 1,316 & 1,115 & 0 & 1,701 & 1,700 \\
2035 & 1,594 & 1,594 & 1,310 & 1,114 & 0 & 1,689 & 1,689 \\
2036 & 1,580 & 1,580 & 1,303 & 1,112 & 0 & 1,673 & 1,673 \\
2037 & 1,573 & 1,573 & 1,298 & 1,109 & 0 & 1,669 & 1,669 \\
2038 & 1,570 & 1,570 & 1,294 & 1,106 & 0 & 1,666 & 1,666 \\
\hline
\end{tabular}
\end{table}
Expand All @@ -3869,20 +3870,20 @@ Catch & Scenario.1 & Scenario.2 & Scenario.3 & Scenario.4 & Scenario.5 & Scenari
\hline
ABC & Scenario.1 & Scenario.2 & Scenario.3 & Scenario.4 & Scenario.5 & Scenario.6 & Scenario.7 \\
\hline
2025 & 2,145 & 2,145 & 1,352 & 980 & 0 & 2,603 & 2,603 \\
2026 & 1,964 & 1,964 & 1,243 & 903 & 0 & 2,377 & 2,377 \\
2027 & 1,793 & 1,793 & 1,123 & 812 & 0 & 1,648 & 1,871 \\
2028 & 1,614 & 1,614 & 1,120 & 846 & 0 & 1,609 & 1,825 \\
2029 & 1,604 & 1,604 & 1,214 & 943 & 0 & 1,682 & 1,761 \\
2030 & 1,570 & 1,570 & 1,247 & 992 & 0 & 1,669 & 1,697 \\
2031 & 1,591 & 1,591 & 1,292 & 1,046 & 0 & 1,696 & 1,704 \\
2032 & 1,598 & 1,598 & 1,318 & 1,083 & 0 & 1,700 & 1,702 \\
2033 & 1,587 & 1,587 & 1,320 & 1,094 & 0 & 1,682 & 1,682 \\
2034 & 1,581 & 1,581 & 1,323 & 1,103 & 0 & 1,674 & 1,674 \\
2035 & 1,567 & 1,567 & 1,314 & 1,101 & 0 & 1,658 & 1,658 \\
2036 & 1,560 & 1,560 & 1,311 & 1,102 & 0 & 1,649 & 1,649 \\
2037 & 1,555 & 1,555 & 1,308 & 1,100 & 0 & 1,646 & 1,646 \\
2038 & 1,551 & 1,551 & 1,303 & 1,097 & 0 & 1,643 & 1,643 \\
2025 & 2,416 & 2,416 & 1,448 & 1,076 & 0 & 2,956 & 2,956 \\
2026 & 2,035 & 2,035 & 1,216 & 904 & 0 & 2,495 & 2,495 \\
2027 & 1,801 & 1,801 & 1,062 & 786 & 0 & 1,578 & 1,835 \\
2028 & 1,594 & 1,594 & 1,067 & 825 & 0 & 1,582 & 1,820 \\
2029 & 1,589 & 1,589 & 1,163 & 922 & 0 & 1,679 & 1,758 \\
2030 & 1,613 & 1,613 & 1,246 & 1,009 & 0 & 1,728 & 1,753 \\
2031 & 1,627 & 1,627 & 1,295 & 1,069 & 0 & 1,736 & 1,742 \\
2032 & 1,616 & 1,616 & 1,309 & 1,095 & 0 & 1,721 & 1,722 \\
2033 & 1,607 & 1,607 & 1,312 & 1,106 & 0 & 1,706 & 1,706 \\
2034 & 1,603 & 1,603 & 1,316 & 1,115 & 0 & 1,701 & 1,700 \\
2035 & 1,594 & 1,594 & 1,310 & 1,114 & 0 & 1,689 & 1,689 \\
2036 & 1,580 & 1,580 & 1,303 & 1,112 & 0 & 1,673 & 1,673 \\
2037 & 1,573 & 1,573 & 1,298 & 1,109 & 0 & 1,669 & 1,669 \\
2038 & 1,570 & 1,570 & 1,294 & 1,106 & 0 & 1,666 & 1,666 \\
\hline
\end{tabular}
\end{table}
Expand All @@ -3895,20 +3896,20 @@ ABC & Scenario.1 & Scenario.2 & Scenario.3 & Scenario.4 & Scenario.5 & Scenario.
\hline
F & Scenario.1 & Scenario.2 & Scenario.3 & Scenario.4 & Scenario.5 & Scenario.6 & Scenario.7 \\
\hline
2025 & 0.213 & 0.213 & 0.213 & 0.213 & 0.213 & 0.213 & 0.213 \\
2026 & 0.235 & 0.235 & 0.235 & 0.235 & 0.235 & 0.463 & 0.364 \\
2027 & 0.364 & 0.364 & 0.214 & 0.150 & 0.000 & 0.407 & 0.349 \\
2028 & 0.362 & 0.362 & 0.214 & 0.150 & 0.000 & 0.420 & 0.444 \\
2029 & 0.347 & 0.347 & 0.214 & 0.150 & 0.000 & 0.413 & 0.420 \\
2030 & 0.339 & 0.339 & 0.214 & 0.150 & 0.000 & 0.406 & 0.408 \\
2031 & 0.337 & 0.337 & 0.214 & 0.150 & 0.000 & 0.405 & 0.405 \\
2032 & 0.335 & 0.335 & 0.214 & 0.150 & 0.000 & 0.404 & 0.404 \\
2033 & 0.334 & 0.334 & 0.214 & 0.150 & 0.000 & 0.401 & 0.401 \\
2034 & 0.333 & 0.333 & 0.214 & 0.150 & 0.000 & 0.399 & 0.399 \\
2035 & 0.333 & 0.333 & 0.214 & 0.150 & 0.000 & 0.399 & 0.399 \\
2036 & 0.332 & 0.332 & 0.214 & 0.150 & 0.000 & 0.398 & 0.397 \\
2037 & 0.331 & 0.331 & 0.214 & 0.150 & 0.000 & 0.397 & 0.397 \\
2038 & 0.331 & 0.331 & 0.214 & 0.150 & 0.000 & 0.396 & 0.396 \\
2025 & 0.198 & 0.198 & 0.198 & 0.198 & 0.198 & 0.198 & 0.198 \\
2026 & 0.241 & 0.241 & 0.241 & 0.241 & 0.241 & 0.513 & 0.394 \\
2027 & 0.394 & 0.394 & 0.214 & 0.154 & 0.000 & 0.440 & 0.371 \\
2028 & 0.391 & 0.391 & 0.214 & 0.154 & 0.000 & 0.464 & 0.491 \\
2029 & 0.376 & 0.376 & 0.214 & 0.154 & 0.000 & 0.459 & 0.466 \\
2030 & 0.366 & 0.366 & 0.214 & 0.154 & 0.000 & 0.450 & 0.452 \\
2031 & 0.363 & 0.363 & 0.214 & 0.154 & 0.000 & 0.446 & 0.447 \\
2032 & 0.361 & 0.361 & 0.214 & 0.154 & 0.000 & 0.445 & 0.445 \\
2033 & 0.360 & 0.360 & 0.214 & 0.154 & 0.000 & 0.442 & 0.442 \\
2034 & 0.358 & 0.358 & 0.214 & 0.154 & 0.000 & 0.440 & 0.440 \\
2035 & 0.358 & 0.358 & 0.214 & 0.154 & 0.000 & 0.440 & 0.440 \\
2036 & 0.357 & 0.357 & 0.214 & 0.154 & 0.000 & 0.438 & 0.438 \\
2037 & 0.357 & 0.357 & 0.214 & 0.154 & 0.000 & 0.437 & 0.437 \\
2038 & 0.356 & 0.356 & 0.214 & 0.154 & 0.000 & 0.437 & 0.437 \\
\hline
\end{tabular}
\end{table}
Expand All @@ -3921,20 +3922,21 @@ F & Scenario.1 & Scenario.2 & Scenario.3 & Scenario.4 & Scenario.5 & Scenario.6
\hline
SSB & Scenario.1 & Scenario.2 & Scenario.3 & Scenario.4 & Scenario.5 & Scenario.6 & Scenario.7 \\
\hline
2025 & 2,955 & 2,955 & 2,955 & 2,955 & 2,955 & 2,955 & 2,955 \\
2026 & 2,635 & 2,635 & 2,635 & 2,635 & 2,635 & 2,484 & 2,548 \\
2027 & 2,483 & 2,483 & 2,568 & 2,604 & 2,694 & 2,103 & 2,274 \\
2028 & 2,469 & 2,469 & 2,781 & 2,931 & 3,339 & 2,186 & 2,329 \\
2029 & 2,483 & 2,483 & 2,934 & 3,172 & 3,878 & 2,239 & 2,296 \\
2030 & 2,488 & 2,488 & 3,019 & 3,329 & 4,319 & 2,251 & 2,271 \\
2031 & 2,496 & 2,496 & 3,075 & 3,440 & 4,691 & 2,257 & 2,262 \\
2032 & 2,504 & 2,504 & 3,111 & 3,517 & 5,004 & 2,260 & 2,261 \\
2033 & 2,504 & 2,504 & 3,125 & 3,560 & 5,252 & 2,258 & 2,257 \\
2034 & 2,486 & 2,486 & 3,112 & 3,566 & 5,422 & 2,240 & 2,240 \\
2035 & 2,474 & 2,474 & 3,100 & 3,565 & 5,550 & 2,230 & 2,230 \\
2036 & 2,460 & 2,460 & 3,084 & 3,556 & 5,644 & 2,217 & 2,217 \\
2037 & 2,453 & 2,453 & 3,073 & 3,548 & 5,712 & 2,213 & 2,213 \\
2038 & 2,466 & 2,466 & 3,082 & 3,559 & 5,777 & 2,227 & 2,227 \\

2025 & 2,949 & 2,949 & 2,949 & 2,949 & 2,949 & 2,949 & 2,949 \\
2026 & 2,624 & 2,624 & 2,624 & 2,624 & 2,624 & 2,445 & 2,521 \\
2027 & 2,467 & 2,467 & 2,566 & 2,600 & 2,690 & 2,051 & 2,238 \\
2028 & 2,460 & 2,460 & 2,807 & 2,942 & 3,344 & 2,173 & 2,318 \\
2029 & 2,493 & 2,493 & 2,983 & 3,196 & 3,886 & 2,249 & 2,300 \\
2030 & 2,503 & 2,503 & 3,079 & 3,356 & 4,328 & 2,262 & 2,278 \\
2031 & 2,500 & 2,500 & 3,130 & 3,458 & 4,700 & 2,253 & 2,257 \\
2032 & 2,502 & 2,502 & 3,161 & 3,527 & 5,013 & 2,252 & 2,252 \\
2033 & 2,502 & 2,502 & 3,175 & 3,566 & 5,259 & 2,251 & 2,251 \\
2034 & 2,485 & 2,485 & 3,162 & 3,570 & 5,428 & 2,234 & 2,234 \\
2035 & 2,471 & 2,471 & 3,149 & 3,567 & 5,555 & 2,222 & 2,222 \\
2036 & 2,455 & 2,455 & 3,132 & 3,556 & 5,649 & 2,208 & 2,208 \\
2037 & 2,449 & 2,449 & 3,121 & 3,547 & 5,715 & 2,204 & 2,204 \\
2038 & 2,463 & 2,463 & 3,130 & 3,558 & 5,780 & 2,219 & 2,219 \\
\hline
\end{tabular}
\end{table}
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