minor tweaks

Pacific-salmon-assess · Jun 12, 2024 · 1475c3e · 1475c3e
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diff --git a/01-introduction.Rmd b/01-introduction.Rmd
@@ -26,7 +26,7 @@ Data on catch and spawner abundance (i.e., escapement) has been collected for we
 
 ### Enhancement 
 
-Enhancement of Fraser Pinks is limited and has primarily occurred via spawning channels to create additional high quality spawning habitat. Records dating back to brood year 1955 show estimates of several million Pink fry migrating out of spawning channels (see data in supplement). 
+Enhancement of Fraser Pinks is limited and has primarily occurred via spawning channels to create additional high quality spawning habitat. Records dating back to brood year 1955 show estimates of several million Pink fry migrating out of spawning channels (see data in the reposity linked in Supplement A). 
 Estimates of outmigration varied in precision with monitoring programs primarily designed for other species. 
 Rotary screw trap sampling and or egg to fry survival estimates were used to generate release numbers.
 Prior to the establishment of the Salmonid Enhancement Program (SEP), salmonid enhancement facilities on the Fraser were managed by the IPSFC and production was limited to incidental stocking in spawning channels (i.e. Seaton, Jones, and Weaver). 

diff --git a/08-figs-tables.Rmd b/08-figs-tables.Rmd
@@ -4,6 +4,12 @@
 knitr::include_graphics(here::here("figure/hatchery-influence.png"))
 ```
 
+(ref:fig-HCRs) Current and alternative (PA alternate) harvest control rules (HCRs). The top panel is the HCR relating target catch to run-size while the bottom panel illustrates the resulting target escapement as a function of run-size. Vertical lines denote Limit ($S_{GEN}$) and Upper Stock (80%$S_{MSY}$) reference points, in run-size units. 
+
+```{r fig-HCRs, fig.cap = "(ref:fig-HCRs)"}
+knitr::include_graphics(here::here("figure/HCRs.png"))
+```
+
 (ref:fig-catch-esc) Spawning escapement and catch from 1959 to present. Resulting exploitation rate is show in red on secondary y-axis.
 ```{r fig-catch-esc, fig.cap = "(ref:fig-catch-esc)"}
 knitr::include_graphics(here::here("figure/catch-esc.png"))
@@ -24,12 +30,6 @@ knitr::include_graphics(here::here("figure/avg-mass.png"))
 knitr::include_graphics(here::here("figure/fwd-sim-schematic.png"))
 ```
 
-(ref:fig-HCRs) Current and alternative (PA alternate) harvest control rules (HCRs). The top panel is the HCR relating target catch to run-size while the bottom panel illustrates the resulting target escapement as a function of run-size. Vertical lines denote Limit ($S_{GEN}$) and Upper Stock (80%$S_{MSY}$) reference points, in run-size units. 
-
-```{r fig-HCRs, fig.cap = "(ref:fig-HCRs)"}
-knitr::include_graphics(here::here("figure/HCRs.png"))
-```
-
 (ref:fig-rec-resid) Recruitment residuals from the Fraser Pink spawner-recruitment relationship over time. Thick black line is the median estimates while the shaded band is the 80th percentile.
 ```{r fig-rec-resid, fig.cap = "(ref:fig-rec-resid)"}
 knitr::include_graphics(here::here("figure/rec-resid.png"))

diff --git a/Supplement-model-check.Rmd b/Supplement-model-check.Rmd
@@ -14,6 +14,12 @@ output:
 bibliography: bib/refs.bib
 ---
 
+<style>
+p.caption {
+ font-size: 0.8em;
+}
+</style>
+
 ```{r setup, echo = FALSE, message = FALSE, warning = FALSE}
 library(tidyverse)
 library(here)
@@ -36,7 +42,14 @@ TV.model.pars <- rstan::extract(TV.stan.fit)
 ```
 
 
-This document describes fits from both state-space Ricker spawner-recruit models used fit in the Research Document *Estimating Precautionary Approach reference points and assessing consequences of harvest control rules for Fraser River Pink Salmon (Oncorhynchus gorbuscha)*. Two Ricker models were fit in this paper that serve different purposes. First, a Ricker model with autoregressive (AR1) recruitment residuals was fit to estimate biological benchmarks ($S_{gen}$, $S_{MSY}$, and $U_{MSY}$), then a model with time-varying productivity (Ricker $\alpha$ parameter) was fit in order to condition the biological submodel on recent population dynamics in the closed-loop forward simulation. Data and code to reproduce the analysis and report is available in this [GitHub repository](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/tree/main), where you can see the [R code](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/blob/main/analysis/R/fit-sr-stan.R) to run the models, and the [models](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/tree/main/analysis/Stan) themselves. 
+This document describes fits from both state-space Ricker spawner-recruit models used fit in the Research Document (**link once published online**:
+
+Glaser, D.M., Connors, B.M., Dionne, K., and Huang, A.M. 2024. Estimating Precautionary
+Approach reference points and assessing consequences of harvest control rules for Fraser
+River Pink Salmon (*Oncorhynchus gorbuscha*). DFO Can. Sci. Advis. Sec. Res. Doc. 2024/**nnn**.
+iv + 31 p.
+
+Two state-space spawner-recruit models were fit in this paper that serve different purposes. First, a Ricker model with autoregressive (AR1) recruitment residuals was fit to estimate biological benchmarks ($S_{gen}$, $S_{MSY}$, and $U_{MSY}$), then a model with time-varying productivity (Ricker $\alpha$ parameter) was fit in order to condition the biological submodel on recent population dynamics in the closed-loop forward simulation. Data and code to reproduce the analysis and report is available in this [GitHub repository](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/tree/main), where you can see the [R code](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/blob/main/analysis/R/fit-sr-stan.R) to run the models, and the [models](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/tree/main/analysis/Stan) themselves. 
 
 # Diagnostics 
 

diff --git a/Supplement-model-check.html b/Supplement-model-check.html
@@ -1478,13 +1478,23 @@ <h4 class="author">Dylan M. Glaser, Brendan M. Connors, Kaitlyn Dionne
 </div>
 
 
+<style>
+p.caption {
+font-size: 0.8em;
+}
+</style>
 <p>This document describes fits from both state-space Ricker
-spawner-recruit models used fit in the Research Document <em>Estimating
-Precautionary Approach reference points and assessing consequences of
-harvest control rules for Fraser River Pink Salmon (Oncorhynchus
-gorbuscha)</em>. Two Ricker models were fit in this paper that serve
-different purposes. First, a Ricker model with autoregressive (AR1)
-recruitment residuals was fit to estimate biological benchmarks (<span class="math inline">\(S_{gen}\)</span>, <span class="math inline">\(S_{MSY}\)</span>, and <span class="math inline">\(U_{MSY}\)</span>), then a model with time-varying
+spawner-recruit models used fit in the Research Document (<strong>link
+once published online</strong>:</p>
+<p>Glaser, D.M., Connors, B.M., Dionne, K., and Huang, A.M. 2024.
+Estimating Precautionary Approach reference points and assessing
+consequences of harvest control rules for Fraser River Pink Salmon
+(<em>Oncorhynchus gorbuscha</em>). DFO Can. Sci. Advis. Sec. Res. Doc.
+2024/<strong>nnn</strong>. iv + 31 p.</p>
+<p>Two state-space spawner-recruit models were fit in this paper that
+serve different purposes. First, a Ricker model with autoregressive
+(AR1) recruitment residuals was fit to estimate biological benchmarks
+(<span class="math inline">\(S_{gen}\)</span>, <span class="math inline">\(S_{MSY}\)</span>, and <span class="math inline">\(U_{MSY}\)</span>), then a model with time-varying
 productivity (Ricker <span class="math inline">\(\alpha\)</span>
 parameter) was fit in order to condition the biological submodel on
 recent population dynamics in the closed-loop forward simulation. Data

diff --git a/resdoc.toc b/resdoc.toc
@@ -5,7 +5,7 @@
 \contentsline {subsection}{\numberline {1.1}BACKGROUND}{1}{subsection.0.1.1}%
 \contentsline {subsubsection}{\numberline {1.1.1}Fraser River Pink salmon}{1}{subsubsection.0.1.1.1}%
 \contentsline {subsubsection}{\numberline {1.1.2}Spawners and Catch}{1}{subsubsection.0.1.1.2}%
-\contentsline {subsubsection}{\numberline {1.1.3}Hatcheries and Enhancement}{1}{subsubsection.0.1.1.3}%
+\contentsline {subsubsection}{\numberline {1.1.3}Enhancement}{1}{subsubsection.0.1.1.3}%
 \contentsline {subsubsection}{\numberline {1.1.4}Current Management and Trends}{2}{subsubsection.0.1.1.4}%
 \contentsline {subsubsection}{\numberline {1.1.5}Fraser Pink Fisheries and Fish Stock Provisions}{3}{subsubsection.0.1.1.5}%
 \contentsline {subsection}{\numberline {1.2}OBJECTIVES}{3}{subsection.0.1.2}%
@@ -25,12 +25,12 @@
 \contentsline {subsubsection}{\numberline {4.4.4}ROBUSTNESS TEST}{9}{subsubsection.0.4.4.4}%
 \contentsline {section}{\numberline {5}RESULTS}{9}{section.0.5}%
 \contentsline {subsection}{\numberline {5.1}MODEL FIT AND DIAGNOSTICS}{9}{subsection.0.5.1}%
-\contentsline {subsection}{\numberline {5.2}BIOLOGICAL BENCHMARKS, STOCK STATUS AND TRENDS}{10}{subsection.0.5.2}%
+\contentsline {subsection}{\numberline {5.2}BIOLOGICAL BENCHMARKS, STOCK STATUS AND TRENDS}{9}{subsection.0.5.2}%
 \contentsline {subsection}{\numberline {5.3}HARVEST CONTROL RULE PERFORMANCE}{10}{subsection.0.5.3}%
 \contentsline {section}{\numberline {6}DISCUSSION}{11}{section.0.6}%
 \contentsline {subsection}{\numberline {6.1}SUMMARY OF KEY FINDINGS}{11}{subsection.0.6.1}%
 \contentsline {subsection}{\numberline {6.2}CAVEATS AND ASSUMPTIONS}{12}{subsection.0.6.2}%
-\contentsline {subsection}{\numberline {6.3}EXCEPTIONAL CIRCUMSTANCES OR ASSESSMENT TRIGGERS FOR THE STOCK}{13}{subsection.0.6.3}%
+\contentsline {subsection}{\numberline {6.3}EXCEPTIONAL CIRCUMSTANCES OR ASSESSMENT TRIGGERS FOR THE STOCK}{12}{subsection.0.6.3}%
 \contentsline {subsection}{\numberline {6.4}AREAS OF POTENTIAL FUTURE WORK}{13}{subsection.0.6.4}%
 \contentsline {section}{\numberline {7}ACKNOWLEDGEMENTS}{14}{section.0.7}%
 \contentsline {section}{\numberline {8}FIGURES}{14}{section.0.8}%