v0.2.0

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 (#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 #426
• Update DESCRIPTION to match release number by @ChristineStawitz-NOAA in #425
• resolved issues causing warnings by @MOshima-PIFSC in #430
• #307: export age comp function by @k-doering-NOAA in #438
• 368 convert fims to a pkgdown site by @Bai-Li-NOAA in #437
• #242 fix codecov calc and upload by @k-doering-NOAA in #436
• 391 feature find a file parser for c++ tests by @msupernaw in #434
• fix: deploying pkgdown by @k-doering-NOAA in #448
• fix: remove set() by @KyleShertzer-NOAA in #451
• Update DESCRIPTION by @peterkuriyama-NOAA in #435
• Remove bias correction/adjustment by @Bai-Li-NOAA in #452
• doc: error and progress logging for information.hpp by @nathanvaughan-NOAA in #424
• fix: refactor parameter constructor by @Bai-Li-NOAA in #455
• doc: logit_steep correction by @ChristineStawitz-NOAA in #463
• refactor add_tmb_to_fims_internal by @msupernaw in #459
• Created get-gtest-codecov to create coverage.xml report for issue #242 by @MOshima-PIFSC in #470
• #441: fix reviewer checklist build trigger, edit checklist by @k-doering-NOAA in #474
• 377 refactor call report f from modelhpp instead of fleet and population by @Andrea-Havron-NOAA in #466
• Changed to by @MOshima-PIFSC in #487
• 411 refactor naming convention of member and local variables in the fleet class by @Bai-Li-NOAA in #476
• Remove test data from fims deterministic folder by @Bai-Li-NOAA in #481
• Update GHA workflows to enforce FIMS installation by @Bai-Li-NOAA in #489
• renamed dimension folded indices to be clearer by @peterkuriyama-NOAA in #480
• rm acomp/index nll tests objects by @ChristineStawitz-NOAA in #491
• Delete test files by @ChristineStawitz-NOAA in #492
• fix: update windows-2019 to windows-latest by @Bai-Li-NOAA in #495
• Create multiple namespaces in FIMS by @k-doering-NOAA in #479
• fix: use expect_equal() for deterministic tests by @Bai-Li-NOAA in #496
• fix: build trigger only on pr being opened by @k-doering-NOAA in #498
• 407 updating log files by @nathanvaughan-NOAA in #499
• Name refactoring for tests, growth, and median by @nathanvaughan-NOAA in #503
• Fix the test for population.CalculateRecruitment() by @Bai-Li-NOAA in #508
• fix: update run google test to use windows latest by @k-doering-NOAA in #511
• refactor: move duplicated code into the test fixture section by @Bai-Li-NOAA in #497
• Fims concurrent by @ChristineStawitz-NOAA in #520
• Remove third party library rapidjson by @Bai-Li-NOAA in #519
• Make Doxygen comment style the same by @k-doering-NOAA in #518
• refactor recruitment deviations to log space by @Andrea-Havron-NOAA in #514
• add documentation to test-fims-estimation by @Andrea-Havron-NOAA in #515
• Added start_year and end_year as slots to FIMSFrame by @kellijohnson-NOAA in #501
• New 464 load module by @Andrea-Havron-NOAA in #526
• make log_obs_error a vector by @ChristineStawitz-NOAA in #532
• Fims vector by @ChristineStawitz-NOAA in #517
• Release mq by @ChristineStawitz-NOAA in #533

New Contributors

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

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