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447e998
revise code and change VBK_seas usage
Rick-Methot-NOAA Dec 22, 2025
33f7cba
Update SS_biofxn.tpl spelling
Dec 29, 2025
9d22d5e
Update SS_biofxn.tpl
Rick-Methot-NOAA Dec 29, 2025
19b08f0
revisions to fix big skate
Rick-Methot-NOAA Dec 30, 2025
1dbf892
fix for growth_timevary
Rick-Methot-NOAA Dec 30, 2025
7df064c
add new warning regarding growth in plusgroup
Rick-Methot-NOAA Dec 31, 2025
e9eb73d
WIP stashing now
Rick-Methot-NOAA Jan 14, 2026
5d1f461
improve description of Linf_decay and add option -997
Rick-Methot-NOAA Feb 27, 2026
e1d66a6
add table mean size by cohort; achieve oneseas-twoseas match
Rick-Methot-NOAA Mar 3, 2026
269a372
revise header format for new table
iantaylor-NOAA Mar 3, 2026
54ad129
review and update seasdur usage
Rick-Methot-NOAA Mar 12, 2026
633106b
more clean-up of the growth code
Rick-Methot-NOAA Mar 12, 2026
33508df
add FATAL warning for AFIX2 > nages
Rick-Methot-NOAA Mar 16, 2026
8e0b5e2
fix problem with growth after lin_grow transition
Rick-Methot-NOAA Mar 24, 2026
bfe5aed
more adjustments to season duration usage
Rick-Methot-NOAA Mar 30, 2026
cbaea21
update parameter names for Cessation
Rick-Methot-NOAA Apr 6, 2026
09a2eb8
prevent mean length shrinkage in Richards, gompertz, and cessation
Rick-Methot-NOAA Apr 16, 2026
eabf9ca
add shrinkage trap and cohort devs to all gorwth types
Rick-Methot-NOAA Apr 28, 2026
0ac8bd1
install libuv1-dev for {kableExtra} (which uses {fs})
Apr 29, 2026
2cec312
Update SS_prelim.tpl
Rick-Methot-NOAA May 4, 2026
6954b4f
add cohort devs and prevent shrink to Cessation
Rick-Methot-NOAA May 12, 2026
589bcaf
adjust plus group updating to use numbers from previous year
Rick-Methot-NOAA May 18, 2026
e1db832
adjust plusgroup calc
Rick-Methot-NOAA May 19, 2026
658c2fa
refactor grtowth such that VBK value is positive and negative is expl…
Rick-Methot-NOAA Jun 2, 2026
fbcc256
tweak settings.json
Rick-Methot-NOAA Jun 2, 2026
d534434
all tests looking good; still need cleanup of extra echoes
Rick-Methot-NOAA Jun 5, 2026
ed9847e
change sign on VBK in Lorenzen M to match growth change
Rick-Methot-NOAA Jun 5, 2026
34d834e
remove extra echoinputs
Rick-Methot-NOAA Jun 15, 2026
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4 changes: 1 addition & 3 deletions .github/workflows/run-ss3-bootstrap.yml
Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,7 @@ jobs:
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install --only-upgrade libstdc++6
sudo apt-get install -y libcurl4-openssl-dev
sudo apt-get install -y libfontconfig1-dev
sudo apt-get install -y libharfbuzz-dev libfribidi-dev
sudo apt-get install -y libcurl4-openssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libuv1-dev pkg-config

- name: Setup R
uses: r-lib/actions/setup-r@v2
Expand Down
4 changes: 1 addition & 3 deletions .github/workflows/test-r4ss-with-ss3.yml
Original file line number Diff line number Diff line change
Expand Up @@ -45,9 +45,7 @@ jobs:
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install --only-upgrade libstdc++6
sudo apt-get install -y libcurl4-openssl-dev
sudo apt-get install -y libfontconfig1-dev
sudo apt-get install -y libharfbuzz-dev libfribidi-dev
sudo apt-get install -y libcurl4-openssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libuv1-dev pkg-config

- name: Setup R
uses: r-lib/actions/setup-r@v2
Expand Down
3 changes: 2 additions & 1 deletion .vscode/settings.json
Original file line number Diff line number Diff line change
Expand Up @@ -2,5 +2,6 @@
"files.associations": {
"*.tpl": "c",
"*.htp": "c"
}
},
"C_Cpp.errorSquiggles": "disabled"
}
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