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Update Opakapaka case study and add back to github.io page #101

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Update Opakapaka case study and add back to github.io page #101

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68c1ac5
convert opakapaka to use new r4ss::ss3_data_to_fims()
iantaylor-NOAA Apr 23, 2026
02efd92
fixes to bad edits in previous opakapaka update
iantaylor-NOAA Apr 24, 2026
0a18089
use main branch of r4ss
iantaylor-NOAA Apr 24, 2026
e04a8f6
a few more changes (including formatting, sorry)
iantaylor-NOAA Apr 24, 2026
777f2d9
make some opakapaka parameters dynamic based on SS3 output
iantaylor-NOAA Apr 29, 2026
01ffb24
add opakapaka back to html table of contents
iantaylor-NOAA Apr 29, 2026
d68cf06
fix module_id for fleets in plots
iantaylor-NOAA Apr 29, 2026
59a26ac
fix recruitment plot, add year_conversion_matrix
iantaylor-NOAA Apr 29, 2026
d79ce54
fix bulletted list formatting
iantaylor-NOAA Apr 29, 2026
09b5ef8
fix issues from copilot review, restore length comp plots
iantaylor-NOAA Apr 30, 2026
339b48f
use correct ʻOkina character in ʻŌpakapaka
iantaylor-NOAA Apr 30, 2026
c1d23cc
update README status for all case studies
iantaylor-NOAA Apr 30, 2026
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2 changes: 1 addition & 1 deletion .devcontainer/devcontainer.json
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
"updatePackages": true
},
"ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
"packages": "dplyr,ggplot2,ggridges,reshape2,remotes,shinystan,tidybayes,tidyr,TMB,github::nmfs-ost/stockplotr,github::noaa-afsc/SparseNUTS,github::NOAA-FIMS/FIMS,github::r4ss/r4ss@convert-data-to-fims",
"packages": "dplyr,ggplot2,ggridges,reshape2,remotes,shinystan,tidybayes,tidyr,TMB,github::nmfs-ost/stockplotr,github::noaa-afsc/SparseNUTS,github::NOAA-FIMS/FIMS,github::r4ss/r4ss",
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"installSystemRequirements": true
},
// option to run rstudio. you can type rserver into the command line to
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2 changes: 1 addition & 1 deletion .github/workflows/render-and-publish.yml
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Expand Up @@ -64,7 +64,7 @@ jobs:
github::stan-dev/shinystan
github::noaa-afsc/SparseNUTS
github::NOAA-FIMS/FIMS
github::r4ss/r4ss@convert-data-to-fims
github::r4ss/r4ss
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- name: Set up Quarto
uses: quarto-dev/quarto-actions/setup@v2
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2 changes: 1 addition & 1 deletion .github/workflows/render.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -84,7 +84,7 @@ jobs:
github::stan-dev/shinystan
github::noaa-afsc/SparseNUTS
github::NOAA-FIMS/FIMS
github::r4ss/r4ss@convert-data-to-fims
github::r4ss/r4ss
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- name: Set up Quarto
uses: quarto-dev/quarto-actions/setup@v2
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9 changes: 5 additions & 4 deletions README.md
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Expand Up @@ -7,10 +7,11 @@ Stock | Status
-- | --
NEFSC yellowtail flounder | working
AFSC GOA pollock | working
SWFSC sardine | working
NWFSC petrale | working
PIFSC opakapaka | working
SEFSC scamp | working
PIFSC ʻŌpakapaka | working
Pacific Hake | working
SWFSC sardine | in development
NWFSC petrale | in development
SEFSC scamp | in development

## How to add a case study

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5 changes: 3 additions & 2 deletions _quarto.yml
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Expand Up @@ -5,6 +5,7 @@ project:
- content/AFSC-GOA-pollock.qmd
- content/NEFSC-yellowtail.qmd
- content/pacific-hake.qmd
- content/PIFSC-opakapaka.qmd

website:
page-navigation: true
Expand Down Expand Up @@ -44,8 +45,8 @@ website:
text: Gulf of Alaska pollock
# - href: content/SWFSC-sardine.qmd
# text: sardine
# - href: content/PIFSC-opakapaka.qmd
# text: Opakapaka
- href: content/PIFSC-opakapaka.qmd
text: ʻŌpakapaka
# - href: content/NWFSC-petrale.qmd
# text: petrale sole
# - href: content/SEFSC-scamp.qmd
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