Laswt changes to SR slides

docs/csas-review/sr-main.Rmd

@@ -456,19 +456,6 @@ class: center
 .link-style1[[2024 Integrated Fisheries Management Plan for Groundfish](https://www.pac.dfo-mpo.gc.ca/fm-gp/mplans/ground-fond-ifmp-pgip-sm-eng.html)]
 ]
 
----
-class: center
-### Spatial Catch by Area
-```{r management-areas, out.width = 900}
-plot_catch_spatial(dat$catch_spatial, 
-                   show_majorbound = TRUE, 
-                   # major_labels = labels,
-                   start_year = base_model$dat$start.yr,
-                   fill_scale = scale_fill_viridis_c(trans = "log10", option = "D"),
-                   colour_scale = scale_colour_viridis_c(trans = "log10", option = "D"))
-
-```
-
 ---
 class: center, bg_arf
 ### At-sea sampling
@@ -514,6 +501,19 @@ class: center, bg_arf_pencil
   <a href="https://stock.adobe.com/images/arrowtooth-flounder-atheresthes-stomas-a-flatfish-from-the-north-pacific-in-top-view/317577516?as_campaign=ftmigration2&as_channel=dpcft&as_campclass=brand&as_source=ft_web&as_camptype=acquisition&as_audience=users&as_content=closure_asset-detail-page">Photo Source</a>
 </div>
 
+---
+class: center
+### Spatial Catch by Area 1996-2023
+
+```{r management-areas, out.width = 900}
+plot_catch_spatial(dat$catch_spatial, 
+                   show_majorbound = TRUE, 
+                   # major_labels = labels,
+                   start_year = base_model$dat$start.yr,
+                   fill_scale = scale_fill_viridis_c(trans = "log10", option = "D"),
+                   colour_scale = scale_colour_viridis_c(trans = "log10", option = "D"))
+
+```
 
 ---
 class: center
@@ -569,8 +569,6 @@ class: center
 
 - is split by sex, and has two commercial trawl fleets (Freezer trawlers and Shoreside).
 
-- MCMC chain of `r f(mcmc_chain_length)`, sampled every `r f(mcmc_sample_freq)`, with burn-in of `r f(mcmc_burn_in)`, leaving `r f(mcmc_actual_samples)` posterior samples for inference
-
 - M fixed at 0.2 for Females and 0.35 for Males
 
 - all parameter estimates were very close to those in Table 6 of the `r ca`
@@ -755,6 +753,15 @@ class: center
 
 .left[
 
+- MCMC chain of `r f(mcmc_chain_length)`, sampled every `r f(mcmc_sample_freq)`, with burn-in of `r f(mcmc_burn_in)`, leaving `r f(mcmc_actual_samples)` posterior samples for inference.
+
+- Traceplots appear stable, without artifacts, as in the `r ca`.
+
+- There is very little autocorrelation in the parameters.
+
+- Catchability parameters show more correlation with each other in this update than in the `r ca`, this is mostly evident in the catchability for the `r qcsss` and the `r hsss` parameters (q1 and q3).
+
+- The pairs plot is Figure 41 in the `r ca`.
 ]
 
 ---
@@ -810,12 +817,18 @@ plot_pairs_mcmc(base_model,
 
 ---
 class: center
-### Catch Projections
+### Catch Projections and Decision Tables
 
 .left[
 
-- DFO Sustainable Fisheries Framework (SFF) reference points could not be used, as the selectivity estimates included non-mature fish which appeared to make the entire stock vulnerable to the stock
-- 
+- DFO Sustainable Fisheries Framework (SFF) reference points could not be used (MSY-based), as the selectivity estimates included non-mature fish which appeared to make the entire stock vulnerable to the stock.
+
+- The LRP is $0.2B_0$, the USR is $0.4B_0$, and the alternative USR $0.35B_0$.
+
+- The catch levels projected were truncated at Fishery management's request to 1kt to 8kt in 1kt increments. In the `r ca`, they were from 1kt to 15kt.
+
+- Decision tables are also opposite of the ones in the `r ca`, as all of the probabilities are of being ***above*** the reference points instead of below.
+
 ]
 
 ---
@@ -940,3 +953,4 @@ plot_ref_points_dist_mcmc(base_model,
                           biomass_col = "B2027",
                           proj_catch_vals = 1:8)
 ```
+

docs/csas-review/sr-main.html

@@ -95,11 +95,6 @@
 .link-style1[[2024 Integrated Fisheries Management Plan for Groundfish](https://www.pac.dfo-mpo.gc.ca/fm-gp/mplans/ground-fond-ifmp-pgip-sm-eng.html)]
 ]
 
----
-class: center
-### Spatial Catch by Area
-<img src="knitr-figs-docx/management-areas-1.png" width="900" style="display: block; margin: auto;" />
-
 ---
 class: center, bg_arf
 ### At-sea sampling
@@ -145,6 +140,11 @@
   <a href="https://stock.adobe.com/images/arrowtooth-flounder-atheresthes-stomas-a-flatfish-from-the-north-pacific-in-top-view/317577516?as_campaign=ftmigration2&as_channel=dpcft&as_campclass=brand&as_source=ft_web&as_camptype=acquisition&as_audience=users&as_content=closure_asset-detail-page">Photo Source</a>
 </div>
 
+---
+class: center
+### Spatial Catch by Area 1996-2023
+
+<img src="knitr-figs-docx/management-areas-1.png" width="900" style="display: block; margin: auto;" />
 
 ---
 class: center
@@ -290,8 +290,6 @@
 
 - is split by sex, and has two commercial trawl fleets (Freezer trawlers and Shoreside).
 
-- MCMC chain of 10,000,000, sampled every 5,000, with burn-in of 1,000, leaving 1,000 posterior samples for inference
-
 - M fixed at 0.2 for Females and 0.35 for Males
 
 - all parameter estimates were very close to those in Table 6 of the 2022 stock assessment
@@ -350,11 +348,11 @@
 
 .left[
 
-- sex-specific lengths continue to be recorded for surveys.
+- sex-specific lengths continue to be recorded for surveys, and show that the population is made up of a greater proportion of larger females than males.
 
 - no length sampling since 2019 for the Shoreside fleet.
 
-- Small number of length samples in 2020 in the Freezer Trawler fleet, then non until 2023 when the new at-sea sampling started (bags of fish frozen at sea and sampled on shore)
+- Small number of length samples in 2020 in the Freezer Trawler fleet, then none until 2023 when the new at-sea sampling started (bags of fish frozen at sea and sampled on shore)
 
 - Survey data show larger females make up more of the samples than males.
 
@@ -379,6 +377,15 @@
 
 .left[
 
+- MCMC chain of 10,000,000, sampled every 5,000, with burn-in of 1,000, leaving 1,000 posterior samples for inference.
+
+- Traceplots appear stable, without artifacts, as in the 2022 stock assessment.
+
+- There is very little autocorrelation in the parameters.
+
+- Catchability parameters show more correlation with each other in this update than in the 2022 stock assessment, this is mostly evident in the catchability for the Queen Charlotte Sound Synoptic Survey and the Hecate Strait Synoptic Survey parameters (q1 and q3).
+
+- The pairs plot is Figure 41 in the 2022 stock assessment.
 ]
 
 ---
@@ -401,12 +408,18 @@
 
 ---
 class: center
-### Catch Projections
+### Catch Projections and Decision Tables
 
 .left[
 
-- DFO Sustainable Fisheries Framework (SFF) reference points could not be used, as the selectivity estimates included non-mature fish which appeared to make the entire stock vulnerable to the stock
-- 
+- DFO Sustainable Fisheries Framework (SFF) reference points could not be used (MSY-based), as the selectivity estimates included non-mature fish which appeared to make the entire stock vulnerable to the stock.
+
+- The LRP is `\(0.2B_0\)`, the USR is `\(0.4B_0\)`, and the alternative USR `\(0.35B_0\)`.
+
+- The catch levels projected were truncated at Fishery management's request to 1kt to 8kt in 1kt increments. In the 2022 stock assessment, they were from 1kt to 15kt.
+
+- Decision tables are also opposite of the ones in the 2022 stock assessment, as all of the probabilities are of being ***above*** the reference points instead of below.
+
 ]
 
 ---
@@ -708,6 +721,7 @@
 ### Projected Relative Biomass in 2027 for Catch in 2026
 
 <img src="knitr-figs-docx/fig-catch-streams-nextyr-nextyr-nextyr-proj-1.png" width="900" style="display: block; margin: auto;" />
+
     </textarea>
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