minor edits from CSAS office

Pacific-salmon-assess · Jul 15, 2024 · a329fb0 · a329fb0
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diff --git a/05-results.Rmd b/05-results.Rmd
@@ -21,7 +21,7 @@ Since then, catch has been reduced and the stock has rebounded to higher levels
 Overall, the Kobe plot suggests the stock is currently being under fished, but attaining the catch goal defined in the HCR can be difficult due to other management considerations. 
 
 The most recent (2023) observation of spawner abundance for Fraser Pink Salmon is `r filter(data, year==2023)$spawn`M, which is well above the USR of 80% $S_{MSY}$ suggesting the stock is in a “healthy” state (Figure \@ref(fig:fig-status)). 
-The stock being considered healthy is consistent with the Wild Salmon Policy rapid status assessment tool that takes data quality and multiple metrics into account [@pestalStateSalmonRapid2023], and which has assessed the stock as in the green with high confidence ([Supplement A](https://zenodo.org/records/12549905)). 
+The stock being considered healthy is consistent with the Wild Salmon Policy rapid status assessment tool that takes data quality and multiple metrics into account [@pestalStateSalmonRapid2023], and which has assessed the stock as in the green with high confidence ([Supplement A](https://doi.org/10.5281/zenodo.12549905)). 
 
 ## HARVEST CONTROL RULE PERFORMANCE 
 

diff --git a/06-discussion.Rmd b/06-discussion.Rmd
@@ -2,7 +2,7 @@
 
 ## SUMMARY OF KEY FINDINGS 
 
-In this working paper we briefly review our current understanding of Fraser River Pink Salmon stock structure and distribution, assessment history, and ecosystem and climate factors affecting the stock. 
+In this research document we briefly review our current understanding of Fraser River Pink Salmon stock structure and distribution, assessment history, and ecosystem and climate factors affecting the stock. 
 We then fit a state-space spawner-recruitment model to available to data to characterize stock dynamics, and derive estimates of biological benchmarks to assess stock status. 
 Lastly, we developed a simple closed-loop simulation model based on recent productivity estimates to quantify future expected biological and fishery performance of the current, an illustrative alternative HCR, and a no fishing scenario. 
 
@@ -48,7 +48,7 @@ In addition to routine re-assessment every 2 generations to ensure stock status
 
 - Stock productivity changes drastically, where the median estimate of time-varying productivity (annual Ricker $\alpha$) falls outside the 50th percentile (i.e., `r recent.a.50s[[1]]`-`r recent.a.50s[[2]]`), of the 3 generation median productivity used to condition our forward simulation; 
 
-- New information becomes available that results in changes to the historical time-series of spawner abundance and catches used in this working paper; or
+- New information becomes available that results in changes to the historical time-series of spawner abundance and catches used in this research document; or
 
 - New information becomes available that results in changes to our understanding of stock-structure (e.g., the current Conservation Unit is split into two) and/or major drivers of stock dynamics. 
 

diff --git a/08-figs-tables.Rmd b/08-figs-tables.Rmd
@@ -40,12 +40,12 @@ knitr::include_graphics(here::here("figure/rec-resid.png"))
 knitr::include_graphics(here::here("figure/tv-alpha.png"))
 ```
 
-(ref:fig-SRR) Fraser Pink Salmon spawner-recruitment relationship. Error bars around points, which are color coded by brood year, and relationship are 80% credible interval while the thick black line is the expected relationship.
+(ref:fig-SRR) Fraser Pink Salmon spawner-recruitment relationship. Error bars around points, which are colour coded by brood year, and relationship are 80% credible interval while the thick black line is the expected relationship.
 ```{r fig-SRR, fig.cap = "(ref:fig-SRR)"}
 knitr::include_graphics(here::here("figure/SRR.png"))
 ```
 
-(ref:fig-kobe) Kobe plot of Fraser Pink status overtime. Years are color coded and the first and last ones are labelled. 80% credible intervals are included for the last year of assessment. 
+(ref:fig-kobe) Kobe plot of Fraser Pink status overtime. Years are colour coded and the first and last ones are labelled. 80% credible intervals are included for the last year of assessment. 
 ```{r fig-kobe, fig.cap = "(ref:fig-kobe)"}
 knitr::include_graphics(here::here("figure/kobe.png"))
 ```
@@ -55,7 +55,7 @@ knitr::include_graphics(here::here("figure/kobe.png"))
 knitr::include_graphics(here::here("figure/recent-status.png"))
 ```
 
-(ref:fig-fwd-SC) Projected Fraser Pink spawners and catch (both in millions of fish; shaded and colored lines) over next 10 years when either the current or alternative illustrative HCRs are applied. Historical escapement and catch (black) are included for reference. Shaded polygons are 80% credible intervals and solid lines are medians. The catch index in right hand panel is defined as the average of the top 3 years of catch from 2001 to present. 
+(ref:fig-fwd-SC) Projected Fraser Pink spawners and catch (both in millions of fish; shaded and coloured lines) over next 10 years when either the current or alternative illustrative HCRs are applied. Historical escapement and catch (black) are included for reference. Shaded polygons are 80% credible intervals and solid lines are medians. The catch index in right hand panel is defined as the average of the top 3 years of catch from 2001 to present. 
 ```{r fig-fwd-SC, fig.cap = "(ref:fig-fwd-SC)"}
 knitr::include_graphics(here::here("figure/fwd-SC.png"))
 ```
@@ -74,6 +74,10 @@ df <- data.frame(Years = c("1957-61", "1963-91", "1993-01", "2003-07", "2009-pre
  "PSC test fishery: escapement derived from seine boats in marine and catch data", 
  "PSC Mission sonar"), 
  CV = c("35%", "25%", "20%", "50%", "10%"))
+
+#hack to make sure "assessment method" looks good
+colnames(df) <- c("Years", "Assessment Method", "CV") 
+
 df |>
 mutate_all(function(x){gsub("%", "\\\\%", x)}) |> #to escape special char latex doesn't like 
 csasdown::csas_table(caption = "(ref:tab-spawner-est-methods)",

diff --git a/10-appendix.Rmd b/10-appendix.Rmd
@@ -5,7 +5,7 @@
 # COMPUTING ENVIRONMENT {#app:a} 
 
 This document aims to be transparent and reproducible. 
-All data and code to reproduce the analysis in the report, and generate it, is available in [this Zenodo hosted](https://zenodo.org/records/12550617) [GitHub repository](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/tree/v1.0?tab=readme-ov-file) 
+All data and code to reproduce the analysis in the report, and generate it, is available in [this Zenodo hosted](https://zenodo.org/doi/10.5281/zenodo.12550616) [GitHub repository](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/tree/v1.0?tab=readme-ov-file) 
 The document describing model diagnostics and some additional figures can be found within the repository at `Supplement-model-check.html`. 
 
 

diff --git a/figure/4-panel.png b/figure/4-panel.png
diff --git a/figure/HCRs.png b/figure/HCRs.png
diff --git a/figure/SRR.png b/figure/SRR.png
diff --git a/figure/avg-mass.png b/figure/avg-mass.png
diff --git a/figure/catch-esc.png b/figure/catch-esc.png
diff --git a/figure/fwd-SC.png b/figure/fwd-SC.png
diff --git a/figure/realized-HCR.png b/figure/realized-HCR.png
diff --git a/figure/recent-tv-SRR.png b/figure/recent-tv-SRR.png
diff --git a/figure/tv-SRR.png b/figure/tv-SRR.png
diff --git a/index.Rmd b/index.Rmd
@@ -42,7 +42,7 @@ cat_no: "Fs70-6/2021-012E-PDF"
 citation_other_language: "Last, F.M. et Smith, A.B. Title Here (*Latin Species Name*). DFO Secr. can. des avis sci. du MPO. Doc. de rech 2019/nnn. iv + 13 p."
 
 abstract: |
- Fraser River Pink Salmon spawn throughout the Fraser Basin in odd-numbered years and the Stock Management Unit is comprised of a single Conservation Unit. Landslides have occurred causing migratory impediments to returning adults at different periods with the most notable being Hells Gate in 1914 and more recently the Big Bar Landslide discovered in 2019. Fraser Pink Salmon marine survival is associated with sea-surface temperatures during early marine life, spring bloom timing, and the North Pacific Current, all of which are expected to change as the North Pacific warms as a result of climate change. Adult body size has declined over time, coincident with increasing abundances of salmon in the North Pacific, which has the potential to impact reproductive output as fecundity scales with female size. We fit a state-space spawner-recruitment model to available data to characterize stock dynamics and derive estimates of biological reference points to assess stock status. We then developed a simple closed-loop simulation model based on recent estimates of productivity to quantify future expected biological and fishery performance of the current harvest control rule (HCR), an illustrative alternative HCR and a no fishing scenario. We estimated the proposed Upper Stock Reference (USR) point of 80% $S_{MSY}$ to be 4.6 million (M) fish (3.64-6.11M; median and 80th percentiles), the Limit Reference Point (LRP) $S_{gen}$ to be 1.72M (1.10-2.70M), and the maximum removal reference rate (RR), $U_{MSY}$ to be 0.56 (0.47-0.63). The most recent (2023) observed estimate of spawner abundance for Fraser Pink Salmon is 9.58M suggesting the Stock Management Unit is in a “healthy” state. The existing HCR for Fraser Pinks has a very low probability (< 5%) of the stock falling below its LRP, and a relatively high probability (87.5%) of spawner abundance being above the USR over the next 10 years. Assuming fisheries fully utilize allowable catch, median annual catch is projected to 10.3M over the same time period. Assessment of an illustrative alternative HCR, which is strictly compliant with DFO’s Precautionary Approach Framework, had similar biological performance and slightly worse fishery performance. A robustness test, where productivity was reduced to 10% of its recent estimate, indicated the current and alternatie HCRs had a 9% and 20% chance, respectively, of the stock falling below its LRPs over the next 10 years. We conclude with recommendations on re-assessment triggers and potential areas to focus future work.
+ Fraser River Pink Salmon spawn throughout the Fraser Basin in odd-numbered years and the Stock Management Unit is comprised of a single Conservation Unit. Landslides have occurred causing migratory impediments to returning adults at different periods with the most notable being Hells Gate in 1914 and more recently the Big Bar Landslide discovered in 2019. Fraser Pink Salmon marine survival is associated with sea-surface temperatures during early marine life, spring bloom timing, and the North Pacific Current, all of which are expected to change as the North Pacific warms as a result of climate change. Adult body size has declined over time, coincident with increasing abundances of salmon in the North Pacific, which has the potential to impact reproductive output as fecundity scales with female size. We fit a state-space spawner-recruitment model to available data to characterize stock dynamics and derive estimates of biological reference points to assess stock status. We then developed a simple closed-loop simulation model based on recent estimates of productivity to quantify future expected biological and fishery performance of the current harvest control rule (HCR), an illustrative alternative HCR and a no fishing scenario. We estimated the proposed Upper Stock Reference (USR) point of 80% $S_{MSY}$ to be 4.6 million (M) fish (3.64-6.11M; median and 80th percentiles), the Limit Reference Point (LRP) $S_{gen}$ to be 1.72M (1.10-2.70M), and the maximum removal reference rate (RR), $U_{MSY}$ to be 0.56 (0.47-0.63). The most recent (2023) observed estimate of spawner abundance for Fraser Pink Salmon is 9.58M and we conclude that the Stock Management Unit is in a “healthy” state. The existing HCR for Fraser Pinks has a very low probability (< 5%) of the stock falling below its LRP, and a relatively high probability (87.5%) of spawner abundance being above the USR over the next 10 years. Assuming fisheries fully utilize allowable catch, median annual catch is projected to be 10.3M over the same time period. Assessment of an illustrative alternative HCR, which is strictly compliant with DFO’s Precautionary Approach Framework, had similar biological performance and slightly worse fishery performance. The results of a robustness test, where productivity was reduced to 10% of its recent estimate, showed that the current and alternate HCRs had a 9% and 20% chance, respectively, of the stock falling below its LRPs over the next 10 years. We conclude with recommendations on re-assessment triggers and potential areas to focus future work.
  
 french_abstract: |
  Voici 

diff --git a/resdoc.toc b/resdoc.toc
@@ -34,7 +34,7 @@
 \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}%
-\contentsline {section}{\numberline {9}TABLES}{24}{section.0.9}%
-\contentsline {section}{\numberline {10}REFERENCES CITED}{28}{section.0.10}%
+\contentsline {section}{\numberline {9}TABLES}{23}{section.0.9}%
+\contentsline {section}{\numberline {10}REFERENCES CITED}{27}{section.0.10}%
 \setcounter {tocdepth}{0}
-\contentsline {chapter}{APPENDIX~A. COMPUTING ENVIRONMENT}{32}{section*.3}%
+\contentsline {chapter}{APPENDIX~A. COMPUTING ENVIRONMENT}{31}{section*.3}%