Ecosyste.ms: Issues

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GitHub / nmfs-stock-synthesis/stock-synthesis issues and pull requests

#530 - Another pull request from johnoel/stock-synthesis

Pull Request - State: open - Opened by johnoel about 1 year ago - 2 comments

#528 - update readme with file name changes for doc

Pull Request - State: closed - Opened by e-gugliotti-NOAA about 1 year ago - 9 comments
Labels: bug

#527 - No link on SS web page ???:

Issue - State: closed - Opened by trevorhutton about 1 year ago

#526 - Wrong link in Release notes October 31, 2023

Issue - State: closed - Opened by cgrandin about 1 year ago - 1 comment

#523 - change repo name to ss3-source-code

Pull Request - State: open - Opened by e-gugliotti-NOAA about 1 year ago

#522 - [Bug]: Access to release note of 3.30.21

Issue - State: closed - Opened by arni-magnusson about 1 year ago - 1 comment

#521 - fix MSY search output with >1 season

Pull Request - State: closed - Opened by Rick-Methot-NOAA about 1 year ago - 2 comments

#520 - Add docker target to build file.

Pull Request - State: closed - Opened by johnoel about 1 year ago - 19 comments

#518 - replace gender with sex in data file comments

Pull Request - State: closed - Opened by e-gugliotti-NOAA about 1 year ago

#517 - [Feature]: Test using new ADMB Docker images for building SS3

Issue - State: open - Opened by iantaylor-NOAA about 1 year ago - 7 comments
Labels: workflows

#516 - [Bug]: Replace the word gender to sex in the comments in the data file

Issue - State: closed - Opened by chantelwetzel-noaa about 1 year ago - 3 comments
Labels: biology

#515 - add sexratio to rebuilder

Pull Request - State: closed - Opened by Rick-Methot-NOAA about 1 year ago - 1 comment

#514 - add mature_bio and mature_num to time_series table

Pull Request - State: closed - Opened by Rick-Methot-NOAA about 1 year ago - 2 comments

#513 - Update add vuln bio

Pull Request - State: closed - Opened by Rick-Methot-NOAA about 1 year ago - 6 comments

#512 - [Feature]: add line to rebuilder output consistent with latest rebuilder version (3.12j)

Issue - State: closed - Opened by brianlangseth-NOAA about 1 year ago - 2 comments
Labels: misc. output, forecast, resolved, change log

#511 - Update ss3-release-template.md without neal

Pull Request - State: closed - Opened by e-gugliotti-NOAA about 1 year ago

#510 - Release v3.30.22 checklist

Issue - State: closed - Opened by e-gugliotti-NOAA about 1 year ago - 2 comments

#509 - modify ssnew text for growth Amax

Pull Request - State: closed - Opened by Rick-Methot-NOAA about 1 year ago

#508 - [Bug]: run fails without useful warning when choosing depletion basis 5=X*dyn_Bzero

Issue - State: closed - Opened by iantaylor-NOAA about 1 year ago - 3 comments
Labels: duplicate, misc. output, resolved

#507 - [Feature]: update dynamic Bzero to work with recdev options 3&4

Issue - State: open - Opened by Rick-Methot-NOAA about 1 year ago
Labels: recruitment, misc. internal calc

#505 - [Bug]: check length-at-age output when settlement is at age 1.

Issue - State: closed - Opened by Rick-Methot-NOAA about 1 year ago - 3 comments
Labels: question, growth

#503 - [Feature]: add option to input matrix of M by year & age

Issue - State: open - Opened by iantaylor-NOAA about 1 year ago
Labels: wishlist, natural mortality

#502 - [Feature]: Add mature_num and mature_bio to the time_series table

Issue - State: closed - Opened by EJDick-NOAA about 1 year ago - 1 comment
Labels: misc. output, resolved, change log

#501 - Fix pr workflows

Pull Request - State: closed - Opened by e-gugliotti-NOAA about 1 year ago
Labels: workflows

#500 - add vuln_bio and max_sel to report

Pull Request - State: closed - Opened by Rick-Methot-NOAA about 1 year ago - 5 comments

#499 - [Feature]: add output of vulnerable biomass and max_sel for each fleet

Issue - State: closed - Opened by Rick-Methot-NOAA about 1 year ago - 1 comment
Labels: fishing mortality, r4ss, resolved, change log, survey_&_Q

#498 - Add generalized gamma index

Pull Request - State: closed - Opened by e-gugliotti-NOAA over 1 year ago

#497 - [Feature]: Add generalized gamma index likelihood

Issue - State: open - Opened by Cole-Monnahan-NOAA over 1 year ago - 7 comments
Labels: wishlist, statistics

#496 - Fix pr open issues workflow

Pull Request - State: closed - Opened by e-gugliotti-NOAA over 1 year ago - 1 comment
Labels: workflows

#495 - Update ss3-pr-open-issues.yml

Pull Request - State: closed - Opened by e-gugliotti-NOAA over 1 year ago

#494 - new fcast year approach

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 8 comments

#493 - [Refactor]: More capable approach for input of Forecast year ranges

Issue - State: closed - Opened by e-gugliotti-NOAA over 1 year ago - 7 comments
Labels: forecast, misc. input, resolved, change log

#492 - #490 adjust sel&rec yr range controls

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago

#491 - repair_check_on_Nparms_in_parfile

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago

#490 - [Refactor]: adjust control of retroyr, recdev_end, and fcast_yrs, also see issue 493

Issue - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 5 comments
Labels: recruitment, forecast, resolved, retro

#489 - revised fore_control 4 to use multiplier

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 1 comment

#488 - correct index usage in expval

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago

#487 - [Refactor]: adjust forecast recr option 4 to use multiplier, also see issue 493

Issue - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 1 comment
Labels: forecast, misc. input, resolved, change log

#486 - [Refactor]: make use of join functions more consistent

Issue - State: open - Opened by Rick-Methot-NOAA over 1 year ago
Labels: wishlist, misc. internal calc

#485 - [Bug]: ForeCatch not quite equal to OFLCatch * buffer

Issue - State: closed - Opened by iantaylor-NOAA over 1 year ago - 6 comments
Labels: wont-fix, misc. output, forecast

#484 - [Bug]: empirical wtatage using wrong time index if >1 season

Issue - State: closed - Opened by Rick-Methot-NOAA over 1 year ago
Labels: bug, biology, resolved, change log, survey_&_Q

#483 - minor text updates

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago

#482 - issue 478 add warning if a time block is set to end in endyr

Pull Request - State: closed - Opened by nschindler-noaa over 1 year ago - 2 comments

#481 - [Feature]: Add capability for seasonal offset in a CPUE catchability

Issue - State: open - Opened by Rick-Methot-NOAA over 1 year ago
Labels: wishlist, time-vary parm, new request

#480 - Add additional compile (or update existing) for Mac OS 13?

Issue - State: open - Opened by iantaylor-NOAA over 1 year ago - 4 comments
Labels: bug, workflows

#479 - predator functional response

Issue - State: open - Opened by Rick-Methot-NOAA over 1 year ago
Labels: wishlist, predator

#478 - add warning if last block is set to end in endyr

Issue - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 7 comments
Labels: time-vary parm, forecast, warnings, resolved, change log, retro

#477 - add badges to README.md

Pull Request - State: closed - Opened by e-gugliotti-NOAA over 1 year ago

#476 - Update README.md

Pull Request - State: closed - Opened by iantaylor-NOAA over 1 year ago - 1 comment

#475 - Link to the SS manual in README.md is broken

Issue - State: closed - Opened by John-R-Wallace-NOAA over 1 year ago - 4 comments

#474 - implement changes and warnings for recr surveys

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 4 comments

#473 - 471 bug gradient issue with forecast recruitment option 3

Pull Request - State: closed - Opened by nschindler-noaa over 1 year ago - 12 comments

#472 - Fcast MGparm averaging year value checks

Pull Request - State: closed - Opened by nschindler-noaa over 1 year ago - 6 comments
Labels: retro

#471 - Late recdevs interact with mean approach for forecast base recruitment

Issue - State: closed - Opened by iantaylor-NOAA over 1 year ago - 19 comments
Labels: forecast, warnings, resolved, change log

#470 - Fix bug in lambda warnings and update echoinput for lambda

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 2 comments

#469 - New lambda entries are getting erroneous range check

Issue - State: closed - Opened by Rick-Methot-NOAA over 1 year ago
Labels: misc. input, resolved

#468 - Fix contributing.md

Pull Request - State: closed - Opened by e-gugliotti-NOAA over 1 year ago
Labels: quick

#467 - F rate log space

Pull Request - State: open - Opened by Rick-Methot-NOAA over 1 year ago

#466 - allow early & late recdevs to be expected value for a recruitment index

Issue - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 4 comments
Labels: recruitment, resolved, change log, survey_&_Q

#463 - fix_control_ssnew_for_2DAR

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 2 comments

#462 - 2DAR output to control.ssnew did not have updated parm value

Issue - State: closed - Opened by Rick-Methot-NOAA over 1 year ago
Labels: bug, misc. output, selectivity, resolved, change log

#461 - Add age range option to 2DAR selectivity

Issue - State: open - Opened by Rick-Methot-NOAA over 1 year ago
Labels: selectivity, new request

#459 - Option to omit age_error definitions

Issue - State: open - Opened by Rick-Methot-NOAA over 1 year ago
Labels: composition, new request

#458 - add gh action that does line by line ss_summary.sso comparison

Issue - State: open - Opened by k-doering-NOAA almost 3 years ago - 4 comments

#457 - Does using ss3 opt instead of safe actually speed up model runs?

Issue - State: open - Opened by k-doering-NOAA over 2 years ago - 11 comments
Labels: question, workflows, Epic: Update to ADMB 13.1

#456 - stop run with est when running with no est fails

Issue - State: open - Opened by k-doering-NOAA over 2 years ago
Labels: workflows

#455 - add test that runs mcmc regression test on a stock synthesis model

Issue - State: open - Opened by k-doering-NOAA almost 3 years ago - 15 comments
Labels: workflows, hard

#454 - improve ss3 workflows

Issue - State: open - Opened by k-doering-NOAA about 3 years ago - 1 comment
Labels: build

#452 - improve build_ss3_warnings github actions

Issue - State: open - Opened by k-doering-NOAA over 2 years ago - 1 comment
Labels: quick, workflows, testing

#449 - evolve R packages related to SS3 to ease installation and streamline/modularize/consolidate

Issue - State: open - Opened by Rick-Methot-NOAA almost 3 years ago - 7 comments
Labels: workflows, r4ss

#448 - Transfer workflows from workflow repo

Pull Request - State: closed - Opened by e-gugliotti-NOAA over 1 year ago - 1 comment
Labels: workflows

#447 - Add workflow send email when close pr

Pull Request - State: closed - Opened by e-gugliotti-NOAA over 1 year ago

#445 - [Feature]: add suggestion to warning files for F_method 2 or 3 to nudge users towards F_method 4

Issue - State: open - Opened by iantaylor-NOAA over 1 year ago
Labels: fishing mortality, warnings, new request

#444 - restoration of 3rd parameter for SRR=7

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 2 comments

#443 - [Bug]: restore 3rd parameter to SRR=7

Issue - State: closed - Opened by Rick-Methot-NOAA over 1 year ago
Labels: bug, recruitment, resolved, change log

#442 - 191 spawner recruitment with a b formulation

Pull Request - State: open - Opened by Rick-Methot-NOAA over 1 year ago - 1 comment

#441 - Update new_issue_template.yml with dropdown boxes

Pull Request - State: closed - Opened by e-gugliotti-NOAA over 1 year ago
Labels: workflows

#440 - Fixes #437 regarding partition warning

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 3 comments

#439 - [Bug]: Different length comp likelihood with partition=2 vs partition=0

Issue - State: closed - Opened by e-gugliotti-NOAA over 1 year ago - 1 comment
Labels: wont-fix, statistics

#438 - [Warnings]: Additional parameter under "timevary Q parameters" for block in "Q_extraSD_Srv_SEAMAP_8"

Issue - State: closed - Opened by e-gugliotti-NOAA over 1 year ago - 1 comment
Labels: question, time-vary parm, survey_&_Q

#437 - [Fix]: Partition warning for lencomp when partition == 2

Issue - State: closed - Opened by e-gugliotti-NOAA over 1 year ago - 15 comments
Labels: bug, composition, warnings, resolved, change log

#436 - fix_compreport_for_sex0

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 16 comments

#435 - [Bug]: duplicate entries for unsexed comps getting written to CompReport.sso

Issue - State: closed - Opened by iantaylor-NOAA over 1 year ago - 2 comments
Labels: bug, misc. output, composition, resolved, change log

#434 - Revised pull request template

Pull Request - State: closed - Opened by e-gugliotti-NOAA over 1 year ago - 6 comments
Labels: workflows

#421 - correct variance problem with SRR = 7 (survivorship)

Pull Request - State: closed - Opened by Rick-Methot-NOAA over 1 year ago

#420 - [Bug]: Error in derived quant variance when SRR is type 7 (survivorship)

Issue - State: closed - Opened by Rick-Methot-NOAA over 1 year ago - 10 comments
Labels: bug, recruitment, resolved, change log

#418 - 179 more control for recr dist in forecast

Pull Request - State: closed - Opened by nschindler-noaa over 1 year ago - 27 comments

#416 - [Refactor]: combine workflows repo with stock-synthesis?

Issue - State: open - Opened by iantaylor-NOAA over 1 year ago - 23 comments
Labels: workflows, build

#412 - [Bug]: init_equ catch using wrong se in multi-season model

Issue - State: closed - Opened by Rick-Methot-NOAA over 1 year ago
Labels: bug, initial F, resolved, change log

#402 - [Bug]: partition weighting not working when ParmSelect > Nfleets

Issue - State: closed - Opened by iantaylor-NOAA almost 2 years ago - 2 comments
Labels: bug, misc. internal calc, resolved

#401 - [Feature]: convert F_parm to log(F_parm)

Issue - State: open - Opened by Rick-Methot-NOAA almost 2 years ago
Labels: initial F, fishing mortality, in progress

#394 - Release v3.30.21 checklist

Issue - State: closed - Opened by e-gugliotti-NOAA almost 2 years ago
Labels: workflows

#382 - [Bug]: Report 19 mature_bio and mature_num == 0

Issue - State: closed - Opened by kellijohnson-NOAA almost 2 years ago - 9 comments
Labels: new request

#369 - [Refactor]: fix warning or update count of warnings in tests

Issue - State: closed - Opened by iantaylor-NOAA over 2 years ago - 3 comments
Labels: resolved

#341 - Allow users to use SSB_unfished as the Bratio denominator

Issue - State: closed - Opened by k-doering-NOAA over 2 years ago - 3 comments
Labels: wont-fix, benchmark - MSY, forecast

#333 - Bug: Main rec devs period < endyr and mean recruitment in forecast period produces bad gradients

Issue - State: closed - Opened by nathanvaughan-NOAA over 2 years ago - 11 comments
Labels: bug, recruitment, forecast, resolved, new request