dogfish-catch-update.Rmd

---
title: "Pacific Spiny Dogfish Catch Update"
author: "Sean C. Anderson^1^, Quang C. Huynh^2^, Lindsay N.K. Davidson^1^, Jacquelynne R. King^1^"
institute: "^1^Pacific Biological Station, Fisheries and Oceans Canada, ^2^Blue Matter Science"
date: "Dec. 17, 2024"
output:
  xaringan::moon_reader:
    css: ["xaringan-themer.css", "theme.css"]
    lib_dir: libs
    nature:
      highlightLines: true
      countIncrementalSlides: false
      ratio: "4:3"
---

```{r preamble, include=FALSE, cache=FALSE}
## Build me with live updates with:
## xaringan::inf_mr()
library(knitr)
xaringanthemer::style_mono_accent(
  base_color = "#202020",
  header_font_google = xaringanthemer::google_font("Raleway"),
  text_font_google = xaringanthemer::google_font("Open Sans"),
  code_font_google = xaringanthemer::google_font("Fira Mono"),
  title_slide_background_size = "14%",
  title_slide_background_position = "50% 90%",
  base_font_size = "20px",
  header_h1_font_size = "2.0rem",
  header_h2_font_size = "1.8rem",
  header_h3_font_size = "1.6rem",
  text_font_size = "1.4rem",
  code_font_size = "1.1rem",
  link_color = "#0047AB"
)
knitr_opts <- list(
  message = FALSE,
  warning = FALSE,
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  dpi = 300,
  out.width = "100%",
  fig.asp = 1 / 1.618,
  cache = TRUE,
  autodep = TRUE,
  cache.comments = TRUE,
  fig.align = "center",
  echo = FALSE
)
do.call(knitr::opts_chunk$set, knitr_opts)
```

# Objectives

1. Summarize changes to the catch data since the RPR meeting

1. Communicate plan for handling longline/trap discard count data

1. Answer questions / discuss any issues with the catch data

1. Gain consensus on catch data for Working Paper / SAR revisions

---

# Out of scope

1. Changes to the model beyond updating the catch data 1996 onwards

1. Changes to the older reconstructed catches from the last assessment

1. Changes to other data in the model

1. Acceptance of the Working Paper

---

# Data comparison

- I compared the catch data as presented at the RPR meeting from 1996-2023 for trawl and 2006--023 for longline and trap gear against a separate SQL query built by Maria Cornthwaite

- Maria's query pulled from `PacHarHL`, `PacHarvSable`, and `GFFOS` databases (`Official_Catch` tables)

- Original RPR data came from `GF_MERGED_CATCH` table in `GFFOS` database

- Data are identical after some minor changes to original data...

---

# Data changes

- Hook and line, longline, and trap discarded counts have been used instead of weight. This issue was identified at the RPR meeting.

---

# Data changes

- Discard weights from the midwater trawl fleet have been added from 1996 to 2006

```{r, out.width="100%"}
include_graphics(here::here("figs/rpr-new-discards.png"))
```

---

# Data changes

- DFO Statistical Area 12 was removed so 3CD5ABCDE catch reflects Pacific Fisheries Management Area (PFMA) areas rather than the Pacific States Marine Fisheries Commission (PSMFC) areas

```{r, out.width="80%"}
include_graphics(here::here("figs/area-12-screen.jpg"))
```

---

# Discard comparison with data presented at RPR

- Bottom trawl identical
- Midwater trawl: data added from 1996-2006; statistical area 12 removed
- Longline: discarded weights originally used by mistake; counts presented here

```{r, out.width="100%"}
include_graphics(here::here("figs/rpr-new-discards.png"))
```

---

# Landings comparison with data presented at RPR

- Bottom trawl and longline/traps identical
- Midwater trawl: tiny changes due to removing statistical area 12

<br>

```{r, out.width="100%"}
include_graphics(here::here("figs/rpr-new-landings.png"))
```

---

#  Landings

```{r, out.width="100%"}
include_graphics(here::here("analysis/knitr-figs-pdf/landed-1.png"))
```

---

#  Landings

```{r, out.width="100%"}
include_graphics(here::here("analysis/knitr-figs-pdf/landed-free-1.png"))
```

---

#  Landings

```{r, out.width="100%"}
include_graphics(here::here("analysis/knitr-figs-pdf/landed-stacked-1.png"))
```

---

#  Discard weights

```{r, out.width="100%"}
include_graphics(here::here("analysis/knitr-figs-pdf/discard-weights-1.png"))
```

---

#  Discard counts

```{r, out.width="100%"}
include_graphics(here::here("analysis/knitr-figs-pdf/discard-counts-1.png"))
```

---

#  Discard counts

```{r, out.width="100%"}
include_graphics(here::here("analysis/knitr-figs-pdf/discard-counts-ind-1.png"))
```

---

#  Average dogfish weight: unsorted commercial longline samples

```{r, out.width="90%"}
include_graphics(here::here("figs/longline-unsorted-weight.png"))
```

---

#  Summed discard weights (illustrative only)

- *If* released dogfish weigh 3.07 kg (6.77 lbs) (average)
- Based on unsorted longline samples in 2009, 2010, 2012, 2013
- Include in SAR/Res Doc figs or show counts only?

```{r, out.width="75%"}
include_graphics(here::here("analysis/knitr-figs-pdf/unnamed-chunk-3-1.png"))
```

---

# Impact on spawning output trajectory

```{r, out.width="90%"}
include_graphics(here::here("figs/catch-rpr-update.png"))
```

---

# Plan

- Update catch data files

- Model longline and trap discards as counts

- Use average "dead dogfish" weight ratios in final 5 years to set "dead dogfish" ratios for projections

- Rerun models and finish revisions

- Include brief summary of what was shown here in Res Doc

- Include catch table at least for 1996 onwards (trawl) and 2006 onwards (longline/trap)