Ecosyste.ms: Issues

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GitHub / ss3sim/ss3sim issues and pull requests

#326 - calculate relative error (RE) automatically before saving results

Issue - State: open - Opened by kellijohnson-NOAA about 3 years ago - 2 comments
Labels: topic: results

#325 - #324: all 0 iterations for a scenario in ss3sim

Pull Request - State: closed - Opened by k-doering-NOAA about 3 years ago

#324 - allow 0 iterations for a scenario in ss3sim summary functions

Issue - State: closed - Opened by k-doering-NOAA about 3 years ago - 1 comment
Labels: scary: bug :lady_beetle:, topic: results

#323 - create a GitHub action to build documentation

Issue - State: closed - Opened by kellijohnson-NOAA about 3 years ago - 3 comments
Labels: type: enhancement, topic: documentation :book:, topic: ghaction

#322 - investigate functionality in ss-sims

Issue - State: open - Opened by kellijohnson-NOAA about 3 years ago
Labels: type --- feature

#321 - combine output from scalar and time series to a single file

Issue - State: open - Opened by kellijohnson-NOAA about 3 years ago - 3 comments
Labels: topic: results, type: development :building_construction:

#320 - r4ss warning `SS_readctl_3.30(echoall = )` deprecated

Issue - State: closed - Opened by kellijohnson-NOAA about 3 years ago
Labels: scary: bug :lady_beetle:

#319 - update terminology according to data_dictionary

Issue - State: open - Opened by kellijohnson-NOAA about 3 years ago
Labels: topic: documentation :book:

#317 - Can't make maturity at 50% length time-varying

Issue - State: open - Opened by ChristineStawitz-NOAA about 3 years ago - 1 comment
Labels: scary: bug :lady_beetle:

#316 - improper time varying parameter writing to the dat file

Issue - State: closed - Opened by ChristineStawitz-NOAA about 3 years ago - 3 comments
Labels: scary: bug :lady_beetle:

#315 - misleading line in vignette about `change_tv` column

Issue - State: closed - Opened by ChristineStawitz-NOAA about 3 years ago - 1 comment
Labels: topic: vignette

#314 - Kotaro Ono's change to add a no estimation option via a new argument

Pull Request - State: closed - Opened by ChristineStawitz-NOAA about 3 years ago - 4 comments

#313 - update to SS3 3.30.18

Issue - State: closed - Opened by kellijohnson-NOAA about 3 years ago - 1 comment
Labels: duplicate

#312 - tidyverse warning msgs

Issue - State: closed - Opened by k-doering-NOAA about 3 years ago
Labels: type: enhancement

#311 - Does ss3sim work with two sex models?

Issue - State: open - Opened by ChristineStawitz-NOAA about 3 years ago - 4 comments
Labels: type: :grey_question:

#310 - Update links to SS3

Issue - State: closed - Opened by kellijohnson-NOAA about 3 years ago
Labels: topic: documentation :book:

#309 - Fix R CMD CHECK warnings and notes

Pull Request - State: closed - Opened by k-doering-NOAA over 3 years ago

#308 - ss.par renamed to ss3.par in OM

Issue - State: open - Opened by k-doering-NOAA over 3 years ago
Labels: topic: OM

#307 - update self testing section of vignette

Issue - State: open - Opened by k-doering-NOAA over 3 years ago
Labels: topic: vignette, status: in progress

#306 - merge Development into master

Pull Request - State: closed - Opened by k-doering-NOAA over 3 years ago

#305 - Change ss3sim branches; just use main

Issue - State: closed - Opened by k-doering-NOAA over 3 years ago - 2 comments
Labels: type: :grey_question:

#304 - Starting OM from .par file

Issue - State: open - Opened by peterkuriyama over 3 years ago - 3 comments
Labels: topic: OM

#303 - add initF functionality

Pull Request - State: closed - Opened by peterkuriyama over 3 years ago - 5 comments

#302 - change_f doesn't account for equilibrium catch F parameters

Issue - State: closed - Opened by k-doering-NOAA over 3 years ago - 2 comments
Labels: scary: bug :lady_beetle:

#301 - Add if statement for change_q

Pull Request - State: closed - Opened by peterkuriyama over 3 years ago - 2 comments

#300 - turn off EM to not estimate

Issue - State: closed - Opened by kellijohnson-NOAA almost 4 years ago - 5 comments
Labels: type: enhancement

#299 - Comments on new code of conduct

Issue - State: closed - Opened by k-doering-NOAA almost 4 years ago - 1 comment
Labels: topic: documentation :book:

#298 - Contrib

Pull Request - State: closed - Opened by kellijohnson-NOAA almost 4 years ago - 1 comment

#297 - Issue 286

Pull Request - State: closed - Opened by k-doering-NOAA almost 4 years ago - 1 comment

#296 - Effective se_log in `sample_index`

Issue - State: closed - Opened by kellijohnson-NOAA almost 4 years ago - 2 comments
Labels: type: enhancement

#295 - Si.seas

Pull Request - State: closed - Opened by kellijohnson-NOAA almost 4 years ago

#294 - Composition sampling is limited to Yr and FltSvy

Issue - State: open - Opened by kellijohnson-NOAA almost 4 years ago - 4 comments
Labels: status --- on hold, type --- feature, topic --- sampling

#293 - seas in sample_index is fixed at 1 and cannot sample a season-specific index

Issue - State: closed - Opened by kellijohnson-NOAA almost 4 years ago
Labels: type: enhancement

#292 - Update the figure on Readme of input/output file structure

Issue - State: closed - Opened by kellijohnson-NOAA almost 4 years ago - 5 comments
Labels: topic: vignette

#291 - Deprecate casefiles and associated functions

Pull Request - State: closed - Opened by k-doering-NOAA almost 4 years ago - 5 comments

#290 - render vignettes and host on github pages

Issue - State: closed - Opened by k-doering-NOAA almost 4 years ago
Labels: topic: vignette

#289 - Validation of a length-based assessment model via ss3sim

Issue - State: open - Opened by sungli211 almost 4 years ago - 4 comments
Labels: type: :grey_question:, topic: documentation :book:

#288 - deprecate case files

Issue - State: closed - Opened by kellijohnson-NOAA almost 4 years ago - 2 comments

#287 - Fixes and refactoring to improve ss3sim when using a simdf

Pull Request - State: closed - Opened by k-doering-NOAA almost 4 years ago

#286 - Allow em rebinning with conditional age at length data

Issue - State: closed - Opened by k-doering-NOAA almost 4 years ago
Labels: type: enhancement

#285 - issues with specifying a om or em dir

Issue - State: closed - Opened by k-doering-NOAA almost 4 years ago - 2 comments
Labels: scary: bug :lady_beetle:

#284 - specifying random F values do not vary among iterations within a scenario

Issue - State: open - Opened by k-doering-NOAA almost 4 years ago
Labels: topic: OM, status: high priority, type: development :building_construction:

#283 - Fix weight comps

Pull Request - State: closed - Opened by k-doering-NOAA about 4 years ago - 5 comments

#282 - Issue running ems when changing start year of fishing

Issue - State: open - Opened by k-doering-NOAA about 4 years ago - 1 comment
Labels: scary: bug :lady_beetle:, topic: EM, status: high priority, type: development :building_construction:

#281 - Update summaries

Pull Request - State: closed - Opened by k-doering-NOAA about 4 years ago - 4 comments

#278 - feat: allow different filenames for summary csvs

Pull Request - State: closed - Opened by k-doering-NOAA over 4 years ago - 2 comments

#277 - Add set of examples using ss3sim

Issue - State: open - Opened by ChristineStawitz-NOAA over 4 years ago - 6 comments
Labels: topic --- vignette, type --- documentation, status --- wip, type --- feature

#276 - return() from copy_ss3models is just for last model

Issue - State: closed - Opened by kellijohnson-NOAA over 4 years ago - 1 comment
Labels: scary: bug :lady_beetle:, topic: OM, topic: EM, type: development :building_construction:

#275 - Remove sapply

Issue - State: closed - Opened by kellijohnson-NOAA over 4 years ago
Labels: topic: style, status: good first issue, type: refactor

#274 - Small fixes for functions called by get_results all

Pull Request - State: closed - Opened by k-doering-NOAA over 4 years ago - 4 comments

#273 - scenarios and init aren't needed in run_ss3model

Issue - State: closed - Opened by kellijohnson-NOAA over 4 years ago
Labels: type: enhancement

#272 - Guidance on troubleshooting poor convergence

Issue - State: open - Opened by Cole-Monnahan-NOAA over 4 years ago - 2 comments
Labels: type: :grey_question:, topic: vignette, topic: documentation :book:, topic: EM, status: high priority

#271 - changes to get_results_all and lower summary functions

Pull Request - State: closed - Opened by k-doering-NOAA over 4 years ago - 1 comment

#269 - Development: add capabilities to use conditional length at age data

Pull Request - State: closed - Opened by k-doering-NOAA almost 5 years ago - 3 comments

#268 - More detailed tutorial?

Issue - State: closed - Opened by mingsun about 5 years ago - 4 comments
Labels: topic: vignette

#267 - Feature request for profile_msy

Issue - State: closed - Opened by colemonnahan about 5 years ago - 1 comment
Labels: type: enhancement

#266 - profile_msy bug

Issue - State: closed - Opened by colemonnahan about 5 years ago - 9 comments
Labels: scary: bug :lady_beetle:

#265 - Add examples for functions missing them

Issue - State: closed - Opened by k-doering-NOAA about 5 years ago - 1 comment
Labels: type: enhancement

#264 - development branch badges on readme show status for master, not development

Issue - State: closed - Opened by k-doering-NOAA about 5 years ago - 3 comments
Labels: topic: documentation :book:

#263 - check standardize_bounds function

Issue - State: closed - Opened by k-doering-NOAA about 5 years ago - 3 comments
Labels: topic: EM, type: development :building_construction:

#262 - make checklist for updating master

Issue - State: closed - Opened by kellijohnson-NOAA about 5 years ago - 1 comment
Labels: topic: documentation :book:

#261 - refactor profile_fmsy to not use .par file

Issue - State: closed - Opened by k-doering-NOAA about 5 years ago - 1 comment
Labels: type: enhancement

#260 - clean up bin

Issue - State: closed - Opened by k-doering-NOAA about 5 years ago - 2 comments

#259 - Don't use Simple model in examples or tests

Issue - State: closed - Opened by k-doering-NOAA about 5 years ago - 1 comment
Labels: type: enhancement

#258 - deprecated dplyr functions used in change_em_binning

Issue - State: closed - Opened by k-doering-NOAA about 5 years ago - 5 comments

#257 - Make sure extdat for 3.30 version is updated to 3.30

Issue - State: closed - Opened by k-doering-NOAA about 5 years ago - 1 comment

#256 - change_F not robust to ctl files with F method = 1 or 3

Issue - State: closed - Opened by k-doering-NOAA over 5 years ago - 4 comments
Labels: scary: bug :lady_beetle:

#255 - Need more unit testing

Issue - State: closed - Opened by k-doering-NOAA over 5 years ago - 6 comments
Labels: type: enhancement

#254 - EM start year leads to different estimates

Issue - State: open - Opened by kellijohnson-NOAA over 5 years ago - 6 comments
Labels: type --- documentation, topic --- EM, status --- wip, type --- feature

#253 - duplicated functionality in sampling composition data

Issue - State: closed - Opened by kellijohnson-NOAA over 5 years ago - 4 comments
Labels: type: enhancement

#252 - check_data survey timing

Issue - State: closed - Opened by kellijohnson-NOAA over 5 years ago

#251 - Errors when no CPUE data

Issue - State: closed - Opened by kellijohnson-NOAA over 5 years ago - 3 comments

#250 - Tests of running ss3 in parallel give errors

Issue - State: closed - Opened by k-doering-NOAA over 5 years ago - 13 comments

#249 - Bugs in examples

Issue - State: closed - Opened by k-doering-NOAA over 5 years ago - 8 comments
Labels: scary: bug :lady_beetle:

#248 - Add cod model from ss3models

Pull Request - State: closed - Opened by k-doering-NOAA over 5 years ago - 8 comments

#247 - find a new name for cod

Issue - State: closed - Opened by kellijohnson-NOAA over 5 years ago - 2 comments

#246 - Errors and warnings from vignette/introduction.Rmd example

Issue - State: closed - Opened by heavywatal almost 6 years ago - 3 comments

#245 - time-varying CV of growth

Issue - State: closed - Opened by kellijohnson-NOAA over 6 years ago - 3 comments

#244 - r4ss version

Issue - State: closed - Opened by kellijohnson-NOAA over 6 years ago - 4 comments

#243 - Example for change_e fails

Issue - State: closed - Opened by iagomosqueira almost 7 years ago - 2 comments

#242 - Sampling updates

Issue - State: open - Opened by kellijohnson-NOAA over 7 years ago - 1 comment
Labels: status: help wanted, type: development :building_construction:, topic: sampling

#241 - path with `get_bin`

Issue - State: closed - Opened by kellijohnson-NOAA over 7 years ago - 2 comments
Labels: scary: bug :lady_beetle:

#240 - Remove complexity from change_e

Issue - State: closed - Opened by kellijohnson-NOAA over 7 years ago - 4 comments
Labels: type: enhancement

#239 - Bug in vignette example with change_tv

Issue - State: closed - Opened by seananderson over 7 years ago - 4 comments

#238 - Pearson residuals for composition data

Issue - State: closed - Opened by colemonnahan almost 8 years ago - 2 comments

#237 - get_results_all doesn't overwrite existing .csv

Issue - State: closed - Opened by cstawitz almost 8 years ago - 8 comments
Labels: type: enhancement

#236 - Inability to turn off estimation of recdevs or recdev bias ramp

Issue - State: closed - Opened by cstawitz almost 8 years ago - 5 comments
Labels: type: :grey_question:

#235 - Package dependencies

Issue - State: closed - Opened by kellijohnson-NOAA about 8 years ago - 8 comments

#234 - Error in parallel execution: foreach call

Issue - State: closed - Opened by cstawitz about 8 years ago - 16 comments

#233 - Add additional clarification to "making models" vignette

Issue - State: closed - Opened by cstawitz over 8 years ago - 11 comments
Labels: topic: vignette

#232 - Fixbin

Pull Request - State: closed - Opened by kellijohnson-NOAA over 8 years ago - 4 comments

#231 - Add option to jitter initial values

Issue - State: closed - Opened by iantaylor-NOAA over 8 years ago - 1 comment
Labels: type: enhancement

#230 - Testing for parameters on bounds is unreliable

Issue - State: open - Opened by colemonnahan over 8 years ago - 8 comments
Labels: type: :grey_question:, topic: documentation :book:, topic: EM, status: low priority

#229 - Minor version update of ss3sim will be submitted to CRAN in a couple days

Issue - State: closed - Opened by seananderson over 8 years ago - 3 comments

#228 - Problem with parallel option

Issue - State: closed - Opened by GwladysLambert over 8 years ago - 12 comments

#227 - Apparent typo in `change_data.r` function

Issue - State: closed - Opened by awhitten over 8 years ago - 8 comments

#226 - Fix show.output.on.console by adding argument to run_ss3model

Pull Request - State: closed - Opened by kellijohnson-NOAA about 9 years ago