niwafisheriesmodelling/casal2 issues and pull requests

#423 - Undefined behaviour when using vector.resize()

Issue - State: open - Opened by Zaita 10 months ago

#422 - Direct floating point equal comparisons

Issue - State: open - Opened by Zaita 10 months ago

#421 - Merge all changes from Alistair Dunn

Pull Request - State: closed - Opened by Zaita 10 months ago - 1 comment

#421 - Merge all changes from Alistair Dunn

Pull Request - State: closed - Opened by Zaita 10 months ago - 1 comment

#420 - Casal2 - Fails to compile on GCC/G++ v13.1.1

Issue - State: open - Opened by Zaita 10 months ago - 1 comment

#419 - Updating the logistic selectivity

Pull Request - State: closed - Opened by agruss2 over 1 year ago - 1 comment

#418 - Update code 202309

Pull Request - State: closed - Opened by agruss2 over 1 year ago

#418 - Update code 202309

Pull Request - State: closed - Opened by agruss2 over 1 year ago

#417 - ADD: new selectivity

Pull Request - State: closed - Opened by Craig44 over 1 year ago

#417 - ADD: new selectivity

Pull Request - State: closed - Opened by Craig44 over 1 year ago

#416 - Simulating abundance or biomass observations with `@catchability.type = nuisance`

Issue - State: open - Opened by Craig44 over 1 year ago

#416 - Simulating abundance or biomass observations with `@catchability.type = nuisance`

Issue - State: open - Opened by Craig44 over 1 year ago

#415 - update readme

Pull Request - State: closed - Opened by Craig44 over 1 year ago

#414 - CASAL2 length based : min_length max_length ?

Issue - State: closed - Opened by fannyouzoulias over 1 year ago - 2 comments

#414 - CASAL2 length based : min_length max_length ?

Issue - State: closed - Opened by fannyouzoulias over 1 year ago - 2 comments

#413 - ReportTabular for type selectivity in an age-based model when the selectivity is length based

Issue - State: open - Opened by Craig44 almost 2 years ago

#413 - ReportTabular for type selectivity in an age-based model when the selectivity is length based

Issue - State: open - Opened by Craig44 almost 2 years ago

#412 - Category format and short hand syntax consideration

Issue - State: open - Opened by Craig44 almost 2 years ago

#412 - Category format and short hand syntax consideration

Issue - State: open - Opened by Craig44 almost 2 years ago

#411 - Nuisance Qs with multiple Indicies

Issue - State: closed - Opened by Craig44 almost 2 years ago

#410 - Time-varying report broken

Issue - State: closed - Opened by Craig44 almost 2 years ago

#410 - Time-varying report broken

Issue - State: closed - Opened by Craig44 almost 2 years ago

#409 - Estimation of vector elements outside the tranformation, when only some elements of that vector are transformed, is not allowed

Issue - State: open - Opened by alistairdunn1 about 2 years ago - 2 comments

#408 - Selectivity class that can change parameterisation over time

Issue - State: open - Opened by Craig44 over 2 years ago - 1 comment

#408 - Selectivity class that can change parameterisation over time

Issue - State: open - Opened by Craig44 over 2 years ago - 1 comment

#407 - Casal2 needs to error out when there are multiple parameter transformations or time-varying blocks on a single addressable

Issue - State: open - Opened by Craig44 over 2 years ago

#407 - Casal2 needs to error out when there are multiple parameter transformations or time-varying blocks on a single addressable

Issue - State: open - Opened by Craig44 over 2 years ago

#406 - CategoryList report not compatiable with Casal2 R library function extract.mpd()

Issue - State: closed - Opened by Craig44 over 2 years ago - 5 comments

#406 - CategoryList report not compatiable with Casal2 R library function extract.mpd()

Issue - State: closed - Opened by Craig44 over 2 years ago - 5 comments

#405 - Dirichlet multinomial

Pull Request - State: closed - Opened by NIWAFisheriesModelling over 2 years ago - 1 comment

#405 - Dirichlet multinomial

Pull Request - State: closed - Opened by NIWAFisheriesModelling over 2 years ago - 1 comment

#404 - Recruitment ycs syntax change 202208

Pull Request - State: closed - Opened by Craig44 over 2 years ago

#404 - Recruitment ycs syntax change 202208

Pull Request - State: closed - Opened by Craig44 over 2 years ago

#403 - ADD: section in usermanual describing syntax changes between releases

Issue - State: open - Opened by Craig44 over 2 years ago

#403 - ADD: section in usermanual describing syntax changes between releases

Issue - State: open - Opened by Craig44 over 2 years ago

#402 - Migrate betadiff casal flags_off into Testmodels before moving out of repo.

Issue - State: closed - Opened by Craig44 over 2 years ago - 2 comments

#402 - Migrate betadiff casal flags_off into Testmodels before moving out of repo.

Issue - State: closed - Opened by Craig44 over 2 years ago - 2 comments

#401 - Dirichlet multinomial likelihood

Issue - State: closed - Opened by Craig44 over 2 years ago - 8 comments

#400 - ADD fishing mortality process, plus improvements 202207

Pull Request - State: closed - Opened by Craig44 over 2 years ago

#399 - ADD: length-based test case: simulated data from the SCI model.

Issue - State: closed - Opened by Craig44 over 2 years ago

#398 - ADD tag test case sexed and unsexed.

Issue - State: open - Opened by Craig44 over 2 years ago - 3 comments

#398 - ADD tag test case sexed and unsexed.

Issue - State: open - Opened by Craig44 over 2 years ago - 3 comments

#397 - Age size observation 202206

Pull Request - State: closed - Opened by Craig44 over 2 years ago

#396 - Add estimate starting values to the `estimate_summary` report

Issue - State: closed - Opened by Craig44 over 2 years ago - 1 comment

#395 - Change ycs_values to be referenced by recruit year rather than spawning year (ycs_year)

Issue - State: closed - Opened by Craig44 over 2 years ago

#394 - Sim casal2 202206

Pull Request - State: closed - Opened by Craig44 over 2 years ago - 1 comment

#394 - Sim casal2 202206

Pull Request - State: closed - Opened by Craig44 over 2 years ago - 1 comment

#393 - Self test functionality idea/Alternatively Write a utility program

Issue - State: open - Opened by Craig44 over 2 years ago

#393 - Self test functionality idea/Alternatively Write a utility program

Issue - State: open - Opened by Craig44 over 2 years ago

#392 - Improve pseudo-observations for reporting output

Issue - State: open - Opened by alistairdunn1 over 2 years ago

#392 - Improve pseudo-observations for reporting output

Issue - State: open - Opened by alistairdunn1 over 2 years ago

#391 - Add Github actions to test base Casal2 R-library

Issue - State: closed - Opened by Craig44 over 2 years ago - 1 comment

#391 - Add Github actions to test base Casal2 R-library

Issue - State: closed - Opened by Craig44 over 2 years ago - 1 comment

#390 - ADD casal2 compatibility check in the R-package to warn users if they should update their R package relative to the casal2.exe

Issue - State: closed - Opened by Craig44 over 2 years ago - 1 comment

#389 - Flagging of penalties in the objective function

Issue - State: closed - Opened by Craig44 almost 3 years ago - 1 comment

#388 - Need to implement mcmc_fixed flag in @estimates

Issue - State: closed - Opened by Craig44 almost 3 years ago

#387 - Run profiles for multiple parameters

Issue - State: open - Opened by Craig44 almost 3 years ago

#386 - Length based model 202204

Pull Request - State: closed - Opened by Craig44 almost 3 years ago

#386 - Length based model 202204

Pull Request - State: closed - Opened by Craig44 almost 3 years ago

#385 - Verifies to add

Issue - State: open - Opened by Craig44 almost 3 years ago

#384 - ADD initial mean length at age into the data table

Issue - State: open - Opened by Craig44 almost 3 years ago

#383 - Automate Simulated observation reports

Issue - State: closed - Opened by Craig44 almost 3 years ago - 1 comment

#383 - Automate Simulated observation reports

Issue - State: closed - Opened by Craig44 almost 3 years ago - 1 comment

#382 - AgeLength Data is incorrectly specified for the attached use case

Issue - State: closed - Opened by Craig44 about 3 years ago

#381 - Test HMC algorithm

Issue - State: closed - Opened by Craig44 about 3 years ago - 1 comment

#380 - Profiling with autodiff libraries errors out

Issue - State: closed - Opened by Craig44 about 3 years ago - 1 comment

#380 - Profiling with autodiff libraries errors out

Issue - State: closed - Opened by Craig44 about 3 years ago - 1 comment

#379 - Initial Addressable transformation change

Pull Request - State: closed - Opened by Craig44 over 3 years ago

#378 - Complete the comparisons of Casal2 and the NOAA stock assessment model comparison project(s)

Issue - State: open - Opened by NIWAFisheriesModelling over 3 years ago

#378 - Complete the comparisons of Casal2 and the NOAA stock assessment model comparison project(s)

Issue - State: open - Opened by NIWAFisheriesModelling over 3 years ago

#377 - Validate the projection functionality with the Test Cases

Issue - State: open - Opened by NIWAFisheriesModelling over 3 years ago

#376 - Add adolc switch 202110

Pull Request - State: closed - Opened by Craig44 over 3 years ago

#375 - Add business rules around the recruitment processes regarding category definitions

Issue - State: closed - Opened by Craig44 over 3 years ago

#375 - Add business rules around the recruitment processes regarding category definitions

Issue - State: closed - Opened by Craig44 over 3 years ago

#373 - Age length redesign 202109

Pull Request - State: closed - Opened by Craig44 over 3 years ago

#371 - merge validation test for modelrunner for multi sim multi par feature.

Pull Request - State: closed - Opened by Craig44 over 3 years ago

#368 - Estimate Transformations need to be added to MCMC iterations

Issue - State: closed - Opened by Zaita over 3 years ago

#367 - Year varying categories produce incorrect answers across many processes/objections

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

#365 - Casal2 MinimiserResult Report is not correct

Issue - State: closed - Opened by Zaita over 3 years ago

#361 - R0 is calculated incorrectly when uising dynamic partition members with the BH_recruitment process

Issue - State: closed - Opened by alistairdunn1 over 3 years ago - 2 comments

#350 - [BUG] Casal2 does not compile on any Linux distros except CentOS 7 and OpenSuSe

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

#350 - [BUG] Casal2 does not compile on any Linux distros except CentOS 7 and OpenSuSe

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

#348 - [BUG] Building standlone versions of Casal2 will not error out if you try to run autodiff in non-autodiff standalone

Issue - State: closed - Opened by Zaita over 3 years ago - 1 comment

#346 - [BUG] Report overwrite flag is appending

Issue - State: closed - Opened by Zaita almost 4 years ago - 1 comment

#344 - [BUG] examples/Simple/Observation.csl2 exists twice with different case sensitivity

Issue - State: closed - Opened by Zaita almost 4 years ago - 1 comment

#338 - Review: casal_initialisation switch maybe unnecessary and superfluous (please check) (Gitlab issue #33)

Issue - State: closed - Opened by largek about 4 years ago - 2 comments