v0.2.0

[ChristineStawitz-NOAA]

What's Changed

Summary of high level/breaking changes:

• Added a pkgdown site for FIMS
• Add code cov tests and site link
• Remove recruitment bias correction and adjustment because we plan to use TMB ([Feature]: Do we need to put bias adjustment fraction within the likelihood? #185)
• Improve logging coverage and separate logs into multiple files
• Put recruitment deviations on the log scale when input
• Report more values with standard errors
• Code cleanup, documentation, and consistency improvements
• Remove rapidjson dependence
• Add start_year and end_year as slots to FIMSFrame
• Make log_obs_error a vector
• Load the Rcpp module upon package install so components don't need to be prefaced by fims$
• Refactor vectors to use fims::Vector class
• Add Newton steps to FIMS integration test to improve convergence in integration test

More detail:

• Update issue forms by @k-doering-NOAA in Update issue forms #426
• Update DESCRIPTION to match release number by @ChristineStawitz-NOAA in Update DESCRIPTION to match release number #425
• resolved issues causing warnings by @MOshima-PIFSC in resolved issues causing warnings #430
• Create R functionality for passing user input to FIMS #307: export age comp function by @k-doering-NOAA in #307: export age comp function #438
• Style code and document by @ChristineStawitz-NOAA in Style code and document #439
• 368 convert fims to a pkgdown site by @Bai-Li-NOAA in 368 convert fims to a pkgdown site #437
• [Bug]: fix code coverage reporting #242 fix codecov calc and upload by @k-doering-NOAA in #242 fix codecov calc and upload #436
• 391 feature find a file parser for c++ tests by @msupernaw in 391 feature find a file parser for c++ tests #434
• Style code and document by @ChristineStawitz-NOAA in Style code and document #440
• fix: deploying pkgdown by @k-doering-NOAA in fix: deploying pkgdown #448
• fix: remove set() by @KyleShertzer-NOAA in fix: remove set() #451
• Update DESCRIPTION by @peterkuriyama-NOAA in Update DESCRIPTION #435
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #454
• Remove bias correction/adjustment by @Bai-Li-NOAA in Remove bias correction/adjustment #452
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #460
• Style code and document by @ChristineStawitz-NOAA in Style code and document #458
• doc: error and progress logging for information.hpp by @nathanvaughan-NOAA in doc: error and progress logging for information.hpp #424
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #461
• fix: refactor parameter constructor by @Bai-Li-NOAA in fix: refactor parameter constructor #455
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #462
• doc: logit_steep correction by @ChristineStawitz-NOAA in doc: logit_steep correction #463
• refactor add_tmb_to_fims_internal by @msupernaw in refactor add_tmb_to_fims_internal #459
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #465
• Created get-gtest-codecov to create coverage.xml report for issue [Bug]: fix code coverage reporting #242 by @MOshima-PIFSC in Created get-gtest-codecov to create coverage.xml report for issue #242 #470
• [Bug]: developer checklist not working as expected #441: fix reviewer checklist build trigger, edit checklist by @k-doering-NOAA in #441: fix reviewer checklist build trigger, edit checklist #474
• 377 refactor call report f from modelhpp instead of fleet and population by @Andrea-Havron-NOAA in 377 refactor call report f from modelhpp instead of fleet and population #466
• Style code and document by @ChristineStawitz-NOAA in Style code and document #484
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #483
• Changed to by @MOshima-PIFSC in Changed <T> to <Type> #487
• 411 refactor naming convention of member and local variables in the fleet class by @Bai-Li-NOAA in 411 refactor naming convention of member and local variables in the fleet class #476
• Remove test data from fims deterministic folder by @Bai-Li-NOAA in Remove test data from fims deterministic folder #481
• Update GHA workflows to enforce FIMS installation by @Bai-Li-NOAA in Update GHA workflows to enforce FIMS installation #489
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #488
• renamed dimension folded indices to be clearer by @peterkuriyama-NOAA in renamed dimension folded indices to be clearer #480
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #490
• rm acomp/index nll tests objects by @ChristineStawitz-NOAA in rm acomp/index nll tests objects #491
• Delete test files by @ChristineStawitz-NOAA in Delete test files #492
• fix: update windows-2019 to windows-latest by @Bai-Li-NOAA in fix: update windows-2019 to windows-latest #495
• Create multiple namespaces in FIMS by @k-doering-NOAA in Create multiple namespaces in FIMS #479
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #500
• fix: use expect_equal() for deterministic tests by @Bai-Li-NOAA in fix: use expect_equal() for deterministic tests #496
• Style code and document by @ChristineStawitz-NOAA in Style code and document #505
• fix: build trigger only on pr being opened by @k-doering-NOAA in fix: build trigger only on pr being opened #498
• 407 updating log files by @nathanvaughan-NOAA in 407 updating log files #499
• Name refactoring for tests, growth, and median by @nathanvaughan-NOAA in Name refactoring for tests, growth, and median #503
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #509
• Fix the test for population.CalculateRecruitment() by @Bai-Li-NOAA in Fix the test for population.CalculateRecruitment() #508
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #512
• fix: update run google test to use windows latest by @k-doering-NOAA in fix: update run google test to use windows latest #511
• refactor: move duplicated code into the test fixture section by @Bai-Li-NOAA in refactor: move duplicated code into the test fixture section #497
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #513
• Fims concurrent by @ChristineStawitz-NOAA in Fims concurrent #520
• Remove third party library rapidjson by @Bai-Li-NOAA in Remove third party library rapidjson #519
• Make Doxygen comment style the same by @k-doering-NOAA in Make Doxygen comment style the same #518
• refactor recruitment deviations to log space by @Andrea-Havron-NOAA in refactor recruitment deviations to log space #514
• add documentation to test-fims-estimation by @Andrea-Havron-NOAA in add documentation to test-fims-estimation #515
• Added start_year and end_year as slots to FIMSFrame by @kellijohnson-NOAA in Added start_year and end_year as slots to FIMSFrame #501
• New 464 load module by @Andrea-Havron-NOAA in New 464 load module #526
• make log_obs_error a vector by @ChristineStawitz-NOAA in make log_obs_error a vector #532
• Fims vector by @ChristineStawitz-NOAA in Fims vector #517
• format C++ code with clang format by @ChristineStawitz-NOAA in format C++ code with clang format #523
• Style code and document by @ChristineStawitz-NOAA in Style code and document #522
• Release mq by @ChristineStawitz-NOAA in Release mq #533

New Contributors

• @peterkuriyama-NOAA made their first contribution in Update DESCRIPTION #435

Full Changelog: v0.1.0...v0.2.0

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This discussion was created from the release v0.2.0.