Skip to content

Commit

Permalink
get 2023 CA length data, working through WA comm catches
Browse files Browse the repository at this point in the history
  • Loading branch information
@okenk
okenk committed Dec 12, 2024
1 parent f420065 commit e7da54e
Show file tree
Hide file tree
Showing 8 changed files with 57 additions and 49 deletions.
40 changes: 24 additions & 16 deletions docs/data_summary_doc.qmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -25,37 +25,43 @@ This documents data streams for use in the Northern Yellowtail Rockfish stock as
Some summary figures:

```{r pacfin-catch, cache=TRUE}
load(here('data/confidential/commercial/pacfin_12-09-2024/PacFIN.YTRK.CompFT.09.Dec.2024.RData'))
load(here('data/confidential/commercial/pacfin_12-11-2024/PacFIN.YTRK.CompFT.11.Dec.2024.RData'))
# I have checked and LANDING_YEAR = PACFIN_YEAR for all rows.
yt_n_catch_pacfin <- catch.pacfin |>
filter(
AGENCY_CODE == 'W' | AGENCY_CODE == 'O' | COUNTY_NAME == 'DEL NORTE' | COUNTY_NAME == 'HUMBOLDT',
LANDING_YEAR < 2024
AGENCY_CODE == 'W' | AGENCY_CODE == 'O' | COUNTY_NAME == 'DEL NORTE' | COUNTY_NAME == 'HUMBOLDT', # OR, WA, N. CA
LANDING_YEAR < 2024,
!(CATCH_AREA_CODE %in% c('23A', '23C', '26A')) # exclude 48 Puget Sound fish tickets
)
# OR landings time series
or_comm_catch <- read.csv(here("Data/Confidential/commercial/Oregon Commercial landings_433_2023.csv")) |>
tibble::as_tibble() |>
group_by(YEAR) |>
summarise(catch_mt = sum(TOTAL))
summarise(catch_mt = sum(TOTAL)) |>
mutate(AGENCY_CODE = 'O')
# WA URCK/UPOP reconstruction
# WA URCK/UPOP reconstruction, use prior to 2000
wa_urck <- read.csv(here('Data/Raw_not_confidential/WA_URCK_UPOP_recon_1981-2016.csv')) |>
filter(Species_AfterComps %in% c('YTRK', 'YTR1')) |>
filter(Species_AfterComps %in% c('YTRK', 'YTR1'),
Year < 2000) |>
group_by(Year) |>
summarise(catch_mt = sum(RoundPounds_AfterComps) * 0.453592 / 1000) |>
mutate(AGENCY_CODE = 'W',
model = 'URCK/UPOP')
mutate(AGENCY_CODE = 'W') |>
rename(YEAR = Year)
# Put it all together
comm_draft_landings <- yt_n_catch_pacfin |>
filter(AGENCY_CODE != 'O') |>
filter(AGENCY_CODE != 'O',
AGENCY_CODE != 'W' | PACFIN_YEAR >= 2000
) |>
group_by(PACFIN_YEAR, AGENCY_CODE)|>
summarise(catch_mt = sum(ROUND_WEIGHT_MTONS)) |>
rename(YEAR = PACFIN_YEAR) |>
bind_rows(
mutate(or_comm_catch, AGENCY_CODE = 'O')
or_comm_catch,
wa_urck
)|>
group_by(YEAR, AGENCY_CODE) |>
summarise(catch_mt = sum(catch_mt)) |>
Expand Down Expand Up @@ -118,14 +124,16 @@ comm_draft_landings |>
bind_rows(
filter(comm2017, AGENCY_CODE == 'W')
)|>
bind_rows(wa_urck) |>
bind_rows(
mutate(wa_urck, model = 'URCK/UPOP')
) |>
ggplot() +
geom_line(aes(x = Year, y = catch_mt, col = model), linewidth = 1) +
viridis::scale_color_viridis(discrete = TRUE) +
labs(title = 'Possible sources for WA landings (vert. line = 1994)', x = 'YEAR') +
geom_vline(xintercept = 1994)
labs(title = 'Possible sources for WA landings (vert. line = 2000)', x = 'YEAR') +
geom_vline(xintercept = 2000)
```
URCK/UPOP = sum of RoundPounds_AfterComps for Species_AfterComps = YTR1 or YTRK, converted to mt.
URCK/UPOP = sum of RoundPounds_AfterComps for Species_AfterComps = YTR1 or YTRK, converted to mt. This is used *instead of* PacFIN catches prior to 2000.

Table of commercial landings by state, 1981 onward.

Expand Down Expand Up @@ -159,7 +167,7 @@ ashop_catch |>

```{r rec-catch-modern}
# WASHINGTON
wa_modern <- read.csv(here('Data/Raw_not_confidential/RecFIN_WA_catch_to_2023.csv')) |>
wa_modern <- read.csv(here('Data/Raw_not_confidential/RecFIN_WA_catch_to_2023.csv')) |>
filter(RECFIN_WATER_AREA_NAME != 'Canada', RECFIN_YEAR <= 2023) |>
tibble::as_tibble() |>
group_by(RECFIN_YEAR) |>
Expand Down Expand Up @@ -298,7 +306,7 @@ For CA rec catch estimates for the assessment:
Initial length sample sizes after running `PacFIN.Utilities::cleanPacFIN()`:

```{r comm-bio, cache=TRUE}
load(here('Data/Confidential/Commercial/pacfin_12-09-2024/PacFIN.YTRK.bds.09.Dec.2024.RData'))
load(here('Data/Confidential/Commercial/pacfin_12-11-2024/PacFIN.YTRK.bds.11.Dec.2024.RData'))
bds_clean <- PacFIN.Utilities::cleanPacFIN(bds.pacfin, verbose = FALSE)
bds_clean |>
filter(state == 'WA' | state == 'OR' | PACFIN_GROUP_PORT_CODE == 'CCA' |
Expand Down
Binary file modified docs/data_summary_doc_files/figure-html/pacfin-catch-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified docs/data_summary_doc_files/figure-html/pacfin-catch-2.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified docs/data_summary_doc_files/figure-html/pacfin-catch-3.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified docs/data_summary_doc_files/figure-html/pacfin-catch-4.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified docs/data_summary_doc_files/figure-html/pacfin-catch-5.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified docs/data_summary_doc_files/figure-html/pacfin-midwater-vs-bottom-figs-1.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
66 changes: 33 additions & 33 deletions docs/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,7 @@ <h2 class="anchored" data-anchor-id="landings">Landings</h2>
<section id="commercial-landings" class="level3">
<h3 class="anchored" data-anchor-id="commercial-landings">Commercial landings</h3>
<p>Some summary figures:</p>
<div class="cell" data-hash="data_summary_doc_cache/html/pacfin-catch_144afba9de0326475e45c80e4e70d7a6">
<div class="cell" data-hash="data_summary_doc_cache/html/pacfin-catch_29edef1b07364eb8e0e56ce0e7b98a7c">
<div class="cell-output-display">
<p><img src="data_summary_doc_files/figure-html/pacfin-catch-1.png" class="img-fluid" width="672"></p>
</div>
Expand All @@ -110,7 +110,7 @@ <h3 class="anchored" data-anchor-id="commercial-landings">Commercial landings</h
<p><img src="data_summary_doc_files/figure-html/pacfin-catch-5.png" class="img-fluid" width="672"></p>
</div>
</div>
<p>URCK/UPOP = sum of RoundPounds_AfterComps for Species_AfterComps = YTR1 or YTRK, converted to mt.</p>
<p>URCK/UPOP = sum of RoundPounds_AfterComps for Species_AfterComps = YTR1 or YTRK, converted to mt. This is used <em>instead of</em> PacFIN catches prior to 2000.</p>
<p>Table of commercial landings by state, 1981 onward.</p>
<div class="cell">
<div class="cell-output-display">
Expand All @@ -128,115 +128,115 @@ <h3 class="anchored" data-anchor-id="commercial-landings">Commercial landings</h
<td style="text-align: left;">1981</td>
<td style="text-align: left;">94.4</td>
<td style="text-align: left;">3633.5</td>
<td style="text-align: left;">5128.3</td>
<td style="text-align: left;">5325.9</td>
</tr>
<tr class="even">
<td style="text-align: left;">1982</td>
<td style="text-align: left;">331.4</td>
<td style="text-align: left;">2960.2</td>
<td style="text-align: left;">5769.4</td>
<td style="text-align: left;">5993.4</td>
</tr>
<tr class="odd">
<td style="text-align: left;">1983</td>
<td style="text-align: left;">105.3</td>
<td style="text-align: left;">3857.1</td>
<td style="text-align: left;">5326.6</td>
<td style="text-align: left;">5812.9</td>
</tr>
<tr class="even">
<td style="text-align: left;">1984</td>
<td style="text-align: left;">357.7</td>
<td style="text-align: left;">2071.7</td>
<td style="text-align: left;">2311.8</td>
<td style="text-align: left;">2574.5</td>
</tr>
<tr class="odd">
<td style="text-align: left;">1985</td>
<td style="text-align: left;">120.2</td>
<td style="text-align: left;">1613.9</td>
<td style="text-align: left;">1347.0</td>
<td style="text-align: left;">1550.5</td>
</tr>
<tr class="even">
<td style="text-align: left;">1986</td>
<td style="text-align: left;">268.9</td>
<td style="text-align: left;">2163.1</td>
<td style="text-align: left;">1982.7</td>
<td style="text-align: left;">2229.1</td>
</tr>
<tr class="odd">
<td style="text-align: left;">1987</td>
<td style="text-align: left;">141.6</td>
<td style="text-align: left;">2484.0</td>
<td style="text-align: left;">1876.9</td>
<td style="text-align: left;">1990.4</td>
</tr>
<tr class="even">
<td style="text-align: left;">1988</td>
<td style="text-align: left;">144.7</td>
<td style="text-align: left;">2613.8</td>
<td style="text-align: left;">2943.5</td>
<td style="text-align: left;">3231.7</td>
</tr>
<tr class="odd">
<td style="text-align: left;">1989</td>
<td style="text-align: left;">354.0</td>
<td style="text-align: left;">2551.0</td>
<td style="text-align: left;">1689.3</td>
<td style="text-align: left;">1814.4</td>
</tr>
<tr class="even">
<td style="text-align: left;">1990</td>
<td style="text-align: left;">466.4</td>
<td style="text-align: left;">2147.3</td>
<td style="text-align: left;">1639.7</td>
<td style="text-align: left;">1725.6</td>
</tr>
<tr class="odd">
<td style="text-align: left;">1991</td>
<td style="text-align: left;">405.8</td>
<td style="text-align: left;">2066.7</td>
<td style="text-align: left;">1140.9</td>
<td style="text-align: left;">1192.4</td>
</tr>
<tr class="even">
<td style="text-align: left;">1992</td>
<td style="text-align: left;">231.9</td>
<td style="text-align: left;">3998.1</td>
<td style="text-align: left;">1327.4</td>
<td style="text-align: left;">1418.3</td>
</tr>
<tr class="odd">
<td style="text-align: left;">1993</td>
<td style="text-align: left;">102.3</td>
<td style="text-align: left;">3090.7</td>
<td style="text-align: left;">2014.4</td>
<td style="text-align: left;">2162.2</td>
</tr>
<tr class="even">
<td style="text-align: left;">1994</td>
<td style="text-align: left;">104.6</td>
<td style="text-align: left;">3215.4</td>
<td style="text-align: left;">1900.9</td>
<td style="text-align: left;">1908.7</td>
</tr>
<tr class="odd">
<td style="text-align: left;">1995</td>
<td style="text-align: left;">115.9</td>
<td style="text-align: left;">3113.7</td>
<td style="text-align: left;">1482.6</td>
<td style="text-align: left;">1482.7</td>
</tr>
<tr class="even">
<td style="text-align: left;">1996</td>
<td style="text-align: left;">153.2</td>
<td style="text-align: left;">3599.3</td>
<td style="text-align: left;">1451.4</td>
<td style="text-align: left;">1451.5</td>
</tr>
<tr class="odd">
<td style="text-align: left;">1997</td>
<td style="text-align: left;">89.6</td>
<td style="text-align: left;">1271.2</td>
<td style="text-align: left;">476.5</td>
<td style="text-align: left;">476.6</td>
</tr>
<tr class="even">
<td style="text-align: left;">1998</td>
<td style="text-align: left;">132.6</td>
<td style="text-align: left;">1744.2</td>
<td style="text-align: left;">617.0</td>
<td style="text-align: left;">617.1</td>
</tr>
<tr class="odd">
<td style="text-align: left;">1999</td>
<td style="text-align: left;">60.9</td>
<td style="text-align: left;">1624.2</td>
<td style="text-align: left;">563.3</td>
<td style="text-align: left;">563.6</td>
</tr>
<tr class="even">
<td style="text-align: left;">2000</td>
Expand Down Expand Up @@ -296,7 +296,7 @@ <h3 class="anchored" data-anchor-id="commercial-landings">Commercial landings</h
<td style="text-align: left;">2009</td>
<td style="text-align: left;">0.6</td>
<td style="text-align: left;">32.4</td>
<td style="text-align: left;">506.3</td>
<td style="text-align: left;">506.2</td>
</tr>
<tr class="even">
<td style="text-align: left;">2010</td>
Expand Down Expand Up @@ -344,31 +344,31 @@ <h3 class="anchored" data-anchor-id="commercial-landings">Commercial landings</h
<td style="text-align: left;">2017</td>
<td style="text-align: left;">4.0</td>
<td style="text-align: left;">1908.6</td>
<td style="text-align: left;">790.0</td>
<td style="text-align: left;">789.7</td>
</tr>
<tr class="even">
<td style="text-align: left;">2018</td>
<td style="text-align: left;">11.0</td>
<td style="text-align: left;">2170.4</td>
<td style="text-align: left;">1026.3</td>
<td style="text-align: left;">1015.4</td>
</tr>
<tr class="odd">
<td style="text-align: left;">2019</td>
<td style="text-align: left;">11.2</td>
<td style="text-align: left;">2214.1</td>
<td style="text-align: left;">1070.2</td>
<td style="text-align: left;">1064.2</td>
</tr>
<tr class="even">
<td style="text-align: left;">2020</td>
<td style="text-align: left;">14.0</td>
<td style="text-align: left;">2264.3</td>
<td style="text-align: left;">1141.6</td>
<td style="text-align: left;">1128.7</td>
</tr>
<tr class="odd">
<td style="text-align: left;">2021</td>
<td style="text-align: left;">28.1</td>
<td style="text-align: left;">1745.7</td>
<td style="text-align: left;">986.9</td>
<td style="text-align: left;">983.8</td>
</tr>
<tr class="even">
<td style="text-align: left;">2022</td>
Expand Down Expand Up @@ -999,7 +999,7 @@ <h2 class="anchored" data-anchor-id="comp-data">Comp Data</h2>
<section id="commercial" class="level3">
<h3 class="anchored" data-anchor-id="commercial">Commercial</h3>
<p>Initial length sample sizes after running <code>PacFIN.Utilities::cleanPacFIN()</code>:</p>
<div class="cell" data-hash="data_summary_doc_cache/html/comm-bio_257620d1f3f2c9faf2cf9f54cf73b453">
<div class="cell" data-hash="data_summary_doc_cache/html/comm-bio_2668abac0d099bc72a3c1078e7275134">
<div class="cell-output cell-output-stdout">
<pre><code> AGE_METHOD1 AGE_METHOD2 AGE_METHOD3 Age method for best age n
1 B B B B 2346
Expand All @@ -1010,7 +1010,7 @@ <h3 class="anchored" data-anchor-id="commercial">Commercial</h3>
6 L &lt;NA&gt; &lt;NA&gt; L 1
7 S &lt;NA&gt; &lt;NA&gt; S 17942
8 T &lt;NA&gt; &lt;NA&gt; T 2
9 &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; 81690</code></pre>
9 &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; &lt;NA&gt; 82197</code></pre>
</div>
<div class="cell-output-display">
<table class="table table-sm table-striped">
Expand Down Expand Up @@ -1397,10 +1397,10 @@ <h3 class="anchored" data-anchor-id="commercial">Commercial</h3>
</tr>
<tr class="even">
<td style="text-align: left;">2021</td>
<td style="text-align: left;">603</td>
<td style="text-align: left;">633</td>
<td style="text-align: left;">1815</td>
<td style="text-align: left;">1157</td>
<td style="text-align: left;">3575</td>
<td style="text-align: left;">3605</td>
</tr>
<tr class="odd">
<td style="text-align: left;">2022</td>
Expand All @@ -1411,10 +1411,10 @@ <h3 class="anchored" data-anchor-id="commercial">Commercial</h3>
</tr>
<tr class="even">
<td style="text-align: left;">2023</td>
<td style="text-align: left;">0</td>
<td style="text-align: left;">302</td>
<td style="text-align: left;">2145</td>
<td style="text-align: left;">1415</td>
<td style="text-align: left;">3560</td>
<td style="text-align: left;">3862</td>
</tr>
</tbody>
</table>
Expand Down

0 comments on commit e7da54e

Please sign in to comment.