latest

_quarto.yml

@@ -15,7 +15,7 @@ project:
 
 website: 
   page-navigation: true
-  title: "Eastern Bering Sea walleye pollock stock assessment" 
+  title: "Assessment of walleye pollock in the eastern Bering Sea" 
   site-url: "https://nmfs-opensci.github.io/NOAA-quarto-simple" 
   repo-url: "https://github.com/afsc-assessments/ebs_pollock_safe"
   repo-actions: [edit, source, issue]
@@ -53,6 +53,7 @@ website:
         #text: Alternative software platforms
       - href: doc/sept.qmd
         text: September 2024 EBS pollock assessment
+
 lightbox: true
 engine: knitr
 date: now
@@ -68,15 +69,15 @@ format:
     toc: true
     toc-title: 'Contents'
     embed-resources: false
-    #numbering: true
-    #number-sections: true
+    #numbering: false
+    #number-sections: false
     code-summary: "Show the code"
     code-fold: true
   pdf:
     documentclass: scrreprt
     papersize: letter
-    #numbering: true
-    #number-sections: true
+    #numbering: false
+    #number-sections: false
     header-includes:
       - \counterwithout{figure}{chapter}
       - \usepackage{fancyhdr}
@@ -100,4 +101,3 @@ filters:
   - include-files.lua
   - quarto
 
-

doc/data/fig_captions.csv

@@ -16,8 +16,8 @@ bts_3d.png,14,bts_3d,Bottom trawl survey pollock catch in kg per hectare for 202
 bts_age_comp.png,15,bts_age,"Pollock abundance levels by age and year as estimated directly from the NMFS bottom-trawl surveys (1990--2019,2021-2024). The 2012 and 2018 year-classes are shaded differently.",,
 avo_map_yr.pdf,16,data_avomap, Maps of acoustic vessel-of-opportunity (AVO) index data 2006-2024. Grid cell size and shading is proportional to pollock backscatter.,,
 vastage.png,17,vastage,Pollock abundance levels by age and year as estimated directly from the NMFS bottom-trawl surveys (1990--2019, 2021--2024) using standard 'design-based' (DB) and VAST approaches.,
-ats_usv.png,18,ats_usv,Geographic dipiction of backscatter intensity as measured from USVs in 2020.,,
-ats_vast.png,19,ats_vast,VAST model predicted log-density of pollock abundance based on acoustic backscatter from NMFS acoustic-trawl surveys (1994--2018) and from the 2020 USV transects.,,
+ATS_maps.png,18,ats_maps,"Heat map of acoustic-trawl survey relative pollock biomass, 2004-2024.",,
+ats_data.png,19,ats_data,"Acoustic-trawl EBS pollock biomass estimates by year used in this assessment. Error bars represent approximate 95% confidence bounds.", 
 fsh_wtage_comb.pdf,20,fsh_wtage_comb,"Recent fishery average weight-at-age anomaly (relative to the mean) by strata for ages 3--10, 2019--2023. Vertical shape reflects uncertainty in the data (wider shapes being more precise), colors are consistent with cohorts.",,
 fsh_wtage_strata,21,fsh_wtage_strata,"Fishery average weight-at-age anomaly (relative to the mean) across strata and combined for all ages (3--10), and available years (1991--2023). Vertical shape reflects uncertainty in the data (wider shapes being more precise), colors are consistent with cohorts.",,
 ,22,fsh_wtage_strata_yr,"Recent fishery average weight-at-age anomaly (relative to the mean) by strata for ages 3--10, 2019--2023. Vertical shape reflects uncertainty in the data (wider shapes being more precise), colors are consistent with cohorts.",,

doc/modeleq.qmd

@@ -19,8 +19,7 @@ total catch biomass $(Y_t)$ can be described as:s
     N_{t+1,A}   &= N_{t,A-1} e^{-Z_{t,A-1}} + N_{t,A} e^{-Z_{t,A}} ,              &1 \le t \le T                \\
     Z_{t,a}     &= F_{t,a} + M_{t,a}                                                                            \\
     C_{t,.}     &= \sum_{a=1}^A{C_{t,a}}                                                                        \\
-    p_{t,a}     &= \frac{C_{t,a} } {C_{t,.} }                                                                   \\
-    Y_{t}       &= \sum_{a=1}^A{w_{t,a}C_{t,a}}                                                                 \\
+    p_{t,a}     &= \frac{C_{t,a} } {C_{t,.} }                                                                   
 \end{align}
 ```
 where
@@ -77,7 +76,6 @@ process as in Dorn et al. (2000):
 ```{=tex}
 \begin{align}
     \delta_t^\mu  -  \delta_{t+1}^\mu     &\sim \mathcal{N}(0,\,\sigma_{\delta^\mu}^{2}) \\
-    \\
     \alpha_t^\mu  -  \alpha_{t+1}^\mu     &\sim \mathcal{N}(0,\,\sigma_{\alpha^\mu}^{2}) \\
     \beta_t^\mu  -  \beta_{t+1}^\mu     &\sim \mathcal{N}(0,\,\sigma_{\beta^\mu}^{2}) 
 \end{align}
@@ -93,9 +91,13 @@ above, but the lognormal penalty was applied to the resulting
 selectivities-at-age directly. The extent of this variability was
 evaluated in the context of the impact on age-specific survey
 catchability/availability and contrasted with an independent estimate of
-pollock availability to the bottom trawl survey. \begin{align}
-    {ln(s_{t,a})}  -  {ln(s_{t+1,a})}  &\sim \mathcal{N}(0,\,\sigma_{sel}^{2}) \\
-\end{align} In 2008 the AT survey selectivity approach was modified. As
+pollock availability to the bottom trawl survey.
+
+\begin{align}
+    {ln(s_{t,a})}  -  {ln(s_{t+1,a})}  &\sim \mathcal{N}(0,\,\sigma_{sel}^{2}) 
+\end{align}
+
+In 2008 the AT survey selectivity approach was modified. As
 an option, the age one pollock observed in this trawl can be treated as
 an index and are not considered part of the age composition (which then
 ranges from age 2-15). This was done to improve some interaction with
@@ -243,7 +245,12 @@ adjusted from the original estimates by the ratio of the expected
 recruitment given spawning biomass (with and without fishing) and the
 estimated stock-recruitment curve. I.e., the recruitment under no
 fishing is modified as:
-$$R_t' = \hat{R}_t\frac{f(B_{t-1}')}{f(B_{t-1})}$$ where $R_t$ is the
+
+\begin{align}
+R_t' = \hat{R}_t\frac{f(B_{t-1}')}{f(B_{t-1})} 
+\end{align}
+
+where $R_t$ is the
 original recruitment estimate in year $t$ with $B_{t-1}'$ and $B_{t-1}$
 representing the stock-recruitment function given spawning biomass under
 no fishing and under the estimated fishing intensity, respectively.
@@ -262,7 +269,9 @@ provides an estimate of the effective number of ages. This is computed for each
 year as a measure of different age groups contributing to the spawning population
 as:
 
- $$ H_i = \exp(-\sum p_a \cdot \log(p_a)) $$
+\begin{align}
+H_i = \exp(-\sum p_a \cdot \log(p_a)) 
+\end{align}
 
 where $p_a$ is the proportion of mature fish biomass-at-age $a$ in year $i$. 
 
@@ -327,9 +336,12 @@ nll(i) = -0.5\sum_{a=1}^A\sum_{t=1}^T{
 \right\}}
 \end{align}
 ```
-where \begin{align}
-\eta_{ta} &=  p_{ta}(1-p_{ta})\\ 
-\text{and} \\
+where 
+\begin{align}
+\eta_{ta} &=  p_{ta}(1-p_{ta}) 
+\end{align}
+and
+\begin{align}
 \tau_t^2 &=  1/n_t 
 \end{align} which gives the variance for $p_{ta}$ \begin{align}
 (\eta_{ta}+0.1/A)\tau_t^2
@@ -377,11 +389,11 @@ nll(i) &= \sum_t{\frac{\ln(u_t^s/\hat N_t^s)^2}{2\sigma_{s,t}^2}}
 optionally biomass) estimate with variance $\sigma_{s,t}$ from survey
 $s$ in year $t$ or optionally, the normal distribution can be selected:
 \begin{align}
-nll(i) &= \sum_t{\frac{(u_t^s - \hat N_t^s)^2}{2\sigma_{s,t}^2}}. \\
+nll(i) &= \sum_t{\frac{(u_t^s - \hat N_t^s)^2}{2\sigma_{s,t}^2}}. 
 \end{align}
 
 The AT survey and AVO index is modeled using a lognormal distribution
-whereas for the BTS survey, a normal distribution was applied.
+whereas for the BTS survey, a multivariate log-normal distribution was applied.
 
 For model configurations in which the BTS data are corrected for
 estimated efficiency, a multivariate lognormal distribution was used.
@@ -433,7 +445,10 @@ each age $i$, $i$= (1, 2,...,15), given actual observed mean and
 variances in weight-at-age over the period 1991-`r thisyr-1`. The values
 of based on available data and (if this option is selected) estimates
 the parameters subject to the natural constraint:
-$$w_{ta}^{future} \sim \mathcal{N}(\bar{w_{a}},\,\sigma_{w_a}^{2})$$
+
+\begin{align}
+w_{ta}^{future} \sim \mathcal{N}(\bar{w_{a}},\,\sigma_{w_a}^{2})
+\end{align}
 
 Note that this converges to the mean values over the time series of data
 (no other likelihood component within the model is affected by future
@@ -448,8 +463,9 @@ data and both cohort and year effects. The model for this is:
 \hat{w}_{ta} &= \bar w_a e^{\upsilon_t} & a=1, \, t \ge 1964 \\
 \hat{w}_{ta} &= \hat{w}_{t-1,a-1} + \Delta_a e^{\psi_t} & a > 1, \, t > 1964 \\
 \Delta_a     &= \bar w_{a+1} - \bar w_a & a<A  \\
-\bar w_a     &= \alpha \left\{L_1+ \left(L_2-L_1\right)\left(\frac{1-K^{a-1}}{1-K^{A-1}}\right)\right\}^3  \\
-\end{align} where the fixed effects parameters are $L_1, L_2, K,$ and
+\bar w_a     &= \alpha \left\{L_1+ \left(L_2-L_1\right)\left(\frac{1-K^{a-1}}{1-K^{A-1}}\right)\right\}^3  
+\end{align} 
+where the fixed effects parameters are $L_1, L_2, K,$ and
 $\alpha$ while the random effects parameters are $\upsilon_t$ and
 $\psi_t$.
 
@@ -478,3 +494,9 @@ presented for the evaluation of $B_{20\%}$) with feedback (via future
 catch specifications) using the control rule and assessment model would
 be required.
 
+## Tier 3 projections
+
+Tier 3 projections were calculated using the projection model where the
+average weight-at-age and selectivity was specified the same way as in
+the Tier 1 calculations but omits estimates of uncertainty in the mean
+recruitment and the selectivity- and weight-at-age values used. 

doc/preamble.tex

@@ -1,10 +1,17 @@
 \usepackage{fancyhdr}
-\usepackage{lipsum}
-\usepackage{lastpage}
+\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
+% \usepackage{lipsum}
+% \usepackage{lastpage}
 \usepackage{booktabs}
 \pagestyle{fancy}
 \fancyhf{}
-\usepackage{booktabs}
 \usepackage{longtable}
 
 \usepackage{rotating}

ebswp.qmd

@@ -1,5 +1,5 @@
 ---
-title: "1. Stock assessment for eastern Bering Sea walleye pollock"
+title: "1. Assessment of walleye pollock in the eastern Bering Sea"
 subtitle: "Draft for November 2024 Plan Team review" 
 author: 
   - name: James Ianelli 
@@ -18,7 +18,7 @@ author:
   - name: Sarah Steinessen
   - name: Carey McGilliard
   - name: Elizabeth Siddon
-date: 11/05/2024
+date: 11/11/2024
 date-format: "MMMM YYYY"
 bibliography: doc/references.bib
 header-includes:
@@ -37,7 +37,6 @@ filters:
   - highlight-text
 format: 
   pdf:
-    #documentclass: article # or `report`, `book`, etc.
     classoption: notitlepage # Ensures title is on the same page as content
     number-pages: TRUE
     number-sections: TRUE
@@ -50,18 +49,17 @@ format:
     extra_dependencies: rotating
     header-includes: 
       - \usepackage{fancyhdr}
-      - \pagestyle{fancy}
+      # - \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
+      - \setlength{\footskip}{4cm} # Lower the footer
 editor_options: 
   chunk_output_type: console
-#css: mystyle.css
 editor: 
   markdown: 
     wrap: 72
@@ -71,19 +69,20 @@ editor:
 <div style="margin-bottom: 1.5in;"></div>
 \vspace{0.5in}
 
-> **This report may be cited as:**  
-> Ianelli, J. et al. 2024. Assessment of the eastern Bering Sea walleye pollock. North Pacific Fishery Management Council, Anchorage, AK. Available [here](https://www.npfmc.org/library/safe-reports/).
 
-<!-- This report may be cited as: Ianelli, J. et al. 2024. Assessment of the eastern -->
-<!-- Bering Sea walleye pollock. North Pacific Fishery Management Council, Anchorage, -->
-<!-- AK. Available [here](https://www.npfmc.org/library/safe-reports/). -->
-<!-- ---------------------- -->
+**This report may be cited as:**  
+Ianelli, J., T. Honkalehto, S. Wassermann,  A. McCarthy, S. Steinessen,
+C. McGilliard, and E. Siddon. 2024. Assessment of walleye pollock in the
+eastern Bering Sea. North Pacific Fishery Management Council,
+Anchorage, AK. Available [here](https://www.npfmc.org/library/safe-reports/).
 
-\vspace{2.5in}
+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
@@ -900,10 +899,11 @@ add transects on the northwestern shelf where historically most
 juveniles have been observed. This resulted in transects at 20 nmi
 spacing between 172° W and the US-Russia maritime boundary. The area
 east of 170°W was surveyed from 11-22 June and west of 170°W was
-surveyed from the 23rd of June through July 17.
+surveyed from the 23rd of June through July 17. The survey estimated densities
+by area are shown in @fig-ATS_maps. 
 
 The survey estimate of pollock for 2024 was 11.4
-billion fish with a biomass of 2.87 million t. This represents a 25%
+billion fish with a biomass of 2.87 million t (@fig-ats_data). This represents a 25%
 decrease in biomass from the 2022 estimate of 3.8 million t (with the 
 abundance estimate at 9.67 billion fish). The 2024 biomass estimate is
 10% below the survey mean of 3.2 million tons for all surveys from 1994-2022.
@@ -4059,14 +4059,15 @@ print(tab,
 byc <- read.csv("doc/data/pollock_catch.csv")[, c(1, 6, 9, 4, 10, 11)]
 
 names(byc) <- c("Year", "target", "gear", "NMFS_area", "Catch", "wed")
-byc <- byc %>% filter(NMFS_area < 540)
+byc <- byc %>% filter(NMFS_area < 540, NMFS_area!=518, NMFS_area>499, target!="")
 ntmp <- unique(byc$target)
+ntmp
 poll <- ntmp[c(1, 5)]
 pcod <- ntmp[c(2)]
 rsole <- ntmp[c(6)]
-yfsole <- ntmp[c(13)]
-oflat <- ntmp[c(3, 7, 9, 15, 16, 17, 18)]
-ospp <- ntmp[c(4, 8, 11, 12, 14)]
+yfsole <- ntmp[c(12)]
+oflat <- ntmp[c(3, 7, 8, 14:17)]
+ospp <- ntmp[c(4, 9, 10, 11, 13)]
 
 byc <- byc %>%
   filter(!target %in% poll) %>%
@@ -4086,6 +4087,7 @@ byc <- byc %>%
   summarise(Catch = sum(Catch), .groups = "drop")
 byc <- byc %>% pivot_wider(names_from = target, values_from = Catch)
 byc <- data.frame(byc)
+byc$Total=rowSums(byc[,2:6],na.rm=TRUE)
 
 # byc <- read.csv("data/byc_of_pollock.csv",header=T)
 for (i in 2:length(byc[1, ])) {
@@ -4275,12 +4277,15 @@ i <- i + 1
 printfig("bts_lenfreq.png", 83)
 #printfig("vastage_vs_db.png", 27)
 # printfig("wtage_bts.png",94);
+printfig("ATS_maps.png", 18)
+printfig("ats_data.pdf", 19)
 printfig("at_age.png", 74)
 printfig("AVO_Series_change.png", 99)
 printfig("cog_AVO_ATS.png", 103)
 printfig("avo_map_yr.png", 16)
 printfig("fsh_lw_month.png", 23)
 printfig("fsh_lw_anom_str_yr_box.png", 24)
+#fsh_lw_anom_yr_box
 printfig("fsh_lw_anom_yr_box.pdf", 25)
 printfig("fsh_wtage_comb.pdf", 20)
 printfig("fsh_wtage_data_pred.png", 88)
@@ -4344,13 +4349,13 @@ printfig("tier3_proj_alt3.png", 54)
 
 \clearpage
 
-<!-- ```{r, results='asis'} -->
-<!-- #| echo: false -->
-<!-- a <- knitr::knit_child("doc/modeleq.qmd", quiet = T) -->
-<!-- cat(a, sep = "\n") -->
-<!-- ``` -->
+```{r, results='asis'} 
+#| echo: false 
+a <- knitr::knit_child("doc/modeleq.qmd", quiet = T) 
+cat(a, sep = "\n") 
+``` 
 
-<!-- \clearpage -->
+\clearpage
 
 ```{r, results='asis'}
 #| echo: false
@@ -4373,7 +4378,7 @@ a <- knitr::knit_child("doc/params.qmd", quiet = T)
 cat(a, sep = "\n")
 ```
 
-<!-- \clearpage -->
+\clearpage
 
 # List of contents, tables and figures {#sec-contents}
 

tools/Do_Plots.R

@@ -41,6 +41,23 @@ if (doplots) {
   p3 + coord_cartesian(ylim = c(0, 7000))
   p3 <- p0/p1 / p2/p3 + plot_layout(axis_titles = "collect");p3
   ggsave("doc/figs/mod_bridge.pdf", plot = p3, width = 6, height = 8.0, units = "in")
+
+ A <- M
+ df <- data.frame(year = A$yr_ats)
+ df$obs  <- A$ob_ats
+ df$pre  <- A$eb_ats
+ df$lb   <- A$ob_ats/exp(2.*sqrt(log(1+(A$sd_ob_ats)^2/(A$ob_ats)^2)))
+ df$ub   <- A$ob_ats*exp(2.*sqrt(log(1+(A$sd_ob_ats)^2/(A$ob_ats)^2)))
+ library(scales);library(ggthemes)
+    p <- ggplot(df) + labs(y = "Acoustic trawl index", x = "Year")
+      p <- p + expand_limits(y = 0)
+      p <- p + geom_point(aes(x=year, y=obs),size=3,color="darkred") +
+        geom_errorbar(aes(x = year, ymax = ub, ymin = lb),width=.5) + 
+    scale_y_continuous(label = comma, limits = c(0, 8600)) + 
+    scale_x_continuous(breaks= seq(1990,2025,by=5)) +  theme_few(base_size = 14)
+      p
+  ggsave("~/_mymods/afsc-assessments/ebs_pollock_safe/doc/figs/ats_data.pdf", 
+         plot = p, width = 8, height = 5.0, units = "in")
 
   #---BTS Fit---------------------
   # Comparing base with 2 vast configurations
@@ -90,11 +107,13 @@ if (doplots) {
 
   p1 <- plot_ats(modlst[c(1,2)]) + ggthemes::theme_few() +
     scale_x_continuous(limits = c(1990, 2025))
+  p1
   ggsave("doc/figs/mod_ats_bridging.pdf", plot = p1, width = 5.2, height = 3.7, units = "in")
 
   #  p1 <- p1+ geom_vline(xintercept=2006.5,color="grey",size=1)
   # p1 <- p1+scale_y_log10()
   p1 <- plot_ats(modlst[c(2)]) + ggthemes::theme_few(base_size = 13)
+  p1
   ggsave("doc/figs/mod_ats_biom.pdf", plot = p1, width = 9.2, height = 3.7, units = "in")
   p1 <- plot_avo(modlst[c(thismod)], ylim = c(0, 5)) + xlim(c(2005, 2025))
   p1 + theme_few(base_size = 19)