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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
bf2ee16
fix sidebar link to acknowledgements
iantaylor-NOAA Jun 8, 2026
1942106
Bump actions/checkout from 6 to 7
dependabot[bot] Jun 22, 2026
dbca67e
fix(case-study): align opakapaka FIMS inputs and diagnostics with cur…
awilnoaa Jun 25, 2026
b4c1f28
cleaning up renv so only one profile
MOshima-PIFSC Jul 10, 2026
27d7e97
convert opakapaka to use new r4ss::ss3_data_to_fims()
iantaylor-NOAA Apr 23, 2026
92f3b7f
fixes to bad edits in previous opakapaka update
iantaylor-NOAA Apr 24, 2026
0ad885d
use main branch of r4ss
iantaylor-NOAA Apr 24, 2026
02068c5
a few more changes (including formatting, sorry)
iantaylor-NOAA Apr 24, 2026
6d31745
make some opakapaka parameters dynamic based on SS3 output
iantaylor-NOAA Apr 29, 2026
edccc1c
add opakapaka back to html table of contents
iantaylor-NOAA Apr 29, 2026
0d0f607
fix module_id for fleets in plots
iantaylor-NOAA Apr 29, 2026
1580688
fix recruitment plot, add year_conversion_matrix
iantaylor-NOAA Apr 29, 2026
8336732
fix bulletted list formatting
iantaylor-NOAA Apr 29, 2026
e35ed8b
fix issues from copilot review, restore length comp plots
iantaylor-NOAA Apr 30, 2026
739cae0
use correct ʻOkina character in ʻŌpakapaka
iantaylor-NOAA Apr 30, 2026
ce53fbb
update README status for all case studies
iantaylor-NOAA Apr 30, 2026
36c07f0
fix(case-study): align opakapaka FIMS inputs and diagnostics with cur…
awilnoaa Jun 25, 2026
7d28d99
Merge branch 'opakapaka-update' of https://github.com/NOAA-FIMS/case-…
MOshima-PIFSC Jul 10, 2026
46d290f
add 1 year forecast to opaka ss3 model
MOshima-PIFSC Jul 11, 2026
149f67f
update to latest version of r4ss
MOshima-PIFSC Jul 11, 2026
aa7a3f9
cleaning up opaka case study
MOshima-PIFSC Jul 11, 2026
332f7b3
add changes to opakapaka for parametric growth from codeclub
iantaylor-NOAA Jul 21, 2026
0cf3255
remove FIMS from lockfile and install vonb branch version
MOshima-PIFSC Jul 22, 2026
9c8ca83
Merge branch 'opakapaka-update' of https://github.com/NOAA-FIMS/case-…
MOshima-PIFSC Jul 22, 2026
473c91d
Making improvements to opaka case study
MOshima-PIFSC Jul 29, 2026
7735736
update plotting code
MOshima-PIFSC Jul 30, 2026
1b2560c
exp recdevs
MOshima-PIFSC Jul 30, 2026
e114bdf
Resolved differences in maturity curve and growth curve
MOshima-PIFSC Aug 4, 2026
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1 change: 1 addition & 0 deletions .Rprofile
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
source("renv/activate.R")
2 changes: 1 addition & 1 deletion .devcontainer/devcontainer.json
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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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iantaylor-NOAA marked this conversation as resolved.
"installSystemRequirements": true
},
// option to run rstudio. you can type rserver into the command line to
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4 changes: 2 additions & 2 deletions .github/workflows/render-and-publish.yml
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Expand Up @@ -12,7 +12,7 @@ jobs:

steps:
- name: Check out repository
uses: actions/checkout@v6
uses: actions/checkout@v7

- name: Set up R (needed for Rmd)
uses: r-lib/actions/setup-r@v2
Expand Down 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
Comment thread
iantaylor-NOAA marked this conversation as resolved.

- name: Set up Quarto
uses: quarto-dev/quarto-actions/setup@v2
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4 changes: 2 additions & 2 deletions .github/workflows/render.yml
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Expand Up @@ -21,7 +21,7 @@ jobs:

steps:
- name: Check out repository
uses: actions/checkout@v6
uses: actions/checkout@v7

- name: Set up R (needed for Rmd)
id: setup-r
Expand Down 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
Comment thread
iantaylor-NOAA marked this conversation as resolved.

- 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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