FIMS Change Log

v0.6.2 (release notes)

  • Fix TMBad windows make file by @Andrea-Havron-NOAA in https://github.com/NOAA-FIMS/FIMS/pull/935
  • Fix bug with uninitialized unfished_biomass by @Andrea-Havron-NOAA in https://github.com/NOAA-FIMS/FIMS/pull/935

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.6.1…v0.6.2

v0.6.1 (release notes)

Thanks to work from @Andrea-Havron-NOAA, @msupernaw, and @Bai-Li-NOAA for investigating the bug that has been persistent since v0.3.0 leading to failed builds on R-universe. This fix, implemented by @Andrea-Havron-NOAA, allows for user and operating system information to be found on more operating systems then we had previously implemented.

v0.6.0 (release notes)

Clang-formatted code to initialize the changes needed for model families. Other than the changes to the names of a few derived quantities and the ungrouped output of get_estimates() users should not see any differences between v0.6.0 and v0.5.3.

v0.5.3 (release notes)

Hotfix to 0.5.2 to fix bug in reshape_output() where there are now fewer rows in the results from get_estimates() because the output from FIMS (via the json file) is now better matched to the output from TMB. Thanks to @KyleShertzer-NOAA for having a plot of selectivity in the scamp case study that was not working correctly anymore, which led to finding this 🐛.

v0.5.1 (release notes)

Hotfix to v0.5.0 to fix pr-commands.yml file, which was leading to a failed GitHub action and emails being sent out to everyone without meaning.

v0.5.0 (release notes)

Release 0.5.0 contains two major features, random effects for the power user and a fits tibble found in the results, e.g., get_fits(fit). See below or the commit messages for more details. - Switch to TMBad from CppAD - Checks that length data has the correct dimension in R - Adds SB to model output - Adds README files to the C++ code - Exports logit functions to R - Functionality was also added to the workflows to allow for better maintenance of the software via GitHub actions

v0.4.0 (release notes)

Release 0.4.0 contains two major features, allowance of catch-per-unit-effort data for fisheries and more information in the estimates tibble found in the results, e.g., get_estimates(fit). See below for more details. - Allows for CPUE data and landings within a single fleet and changes the composition data to be separate from the catch. If there are catches, compositions are based on F, if you have survey compositions those are scaled by q, and you can also have composition data without catch or CPUE and those match the population. - Fixes bug in finalize() where variables were going out of scope by using a shared pointer and RealVector, which allows for estimates tibble to return more. Output is integrated between json and TMB using reshape_tmb_estimates(), reshape_json_estimates(), and reshape_json_derived_quantities(). ParameterVector are now set using resize() and purrr::walk() rather than methods::new(). - Increases code coverage - Restructures R tests using use_testthat_template() - Starts to use Rcpp::Rcerr instead of Rcpp::Rcout - Skips parallel and distribution rcpp test - Adds FIMS_dmultinom() distribution to match TMB - Fixes bug in get_number_of_parameters(). - Uses static_cast([-0-9.]+) to wrap constant variables. - Fixes cmake_minimum_required to use a range and updates googletest version. - Adds minimal fims-demo vignette. - Removes unused estimated_log_M and estimated_log_init_naa from inst/include/interface/rcpp/rcpp_objects/rcpp_population.hpp. - Adds gdb to the devcontainer.json file. - Fixes broken model comparison project links. - Adds dependabot.yml file to update GitHub actions. - Combine initialize_comp() functions.

v0.3.0.1 (release notes)

Fixes errors in the R code found while working on the case studies.

  • cli::cli_abort() messages were not formatted correctly when using pluralism capability
  • uncertainty in the multinomial is multiplied by value within the wrapper functions, which lead to non -999 values. Now, if a -999 is present, it is multiplied by 1 and if not then value is multiplied by uncertainty.

v0.3.0 (release notes)

What’s Changed

Summary of high level/breaking changes:

  • Fits to length data using an age-to-length-conversion matrix, data1 includes the necessary information needed to fit to both ages and lengths.
  • Adds C++ ParameterVector to allow for the estimation of time-varying parameters.
  • Implements R wrapper functions to facilitate
    • creating the input model specifications with create_default_-(), update_parameters(), and initialize_-();
    • adding -999 to the missing fleet, year, age, length, etc. combinations;
    • running the model with a user-supplied argument of n_of_loops, where the default is three, to restart the optimizer from the previous run of nlmimb;
    • summarizing the output with the FIMSFit() function and class.
  • Implements a switch for global verbosity within FIMS through the use of {cli} messages and warnings.
  • Updates the logging system complete with a vignette about how to use it, the logging system can be used for both R and C++ errors, warnings, and information.
  • Creates the initial infrastructure to implement random effects with density functions.
  • Implements a helper function to get the parameter names from the C++ code and populate the results with those names.
  • Makes lpdf_vec return 0 if data is missing.

More detail: See the commit message for this release or the full changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.2.0…v0.3.0.

v0.2.0 (release notes)

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

New Contributors

  • @peterkuriyama-NOAA made their first contribution in https://github.com/NOAA-FIMS/FIMS/pull/435

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.1.0…v0.2.0

v0.1.0.0 (release notes)

This is the first version of the Fisheries Integrated Modeling System (FIMS). At this stage, FIMS can be used to estimate a simple age-structured population model such as case 0 in Li et al. (2021)’s manuscript. Please refer to the collaborative workflow for a description of the model functionality and completeness. Documentation can be found here.

Full Changelog: https://github.com/NOAA-FIMS/FIMS/commits/v0.1.0