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Recent Releases of FIMS

FIMS - v0.6.3

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 10 months ago

FIMS - v0.6.2

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

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 11 months ago

FIMS - v0.6.1

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.

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 11 months ago

FIMS - v0.6.0

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.

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 11 months ago

FIMS - v0.5.3

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 🐛.

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 11 months ago

FIMS - v0.5.1

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.

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 11 months ago

FIMS - v0.5.0

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

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 12 months ago

FIMS - v0.4.0

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.

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA about 1 year ago

FIMS - v0.3.0.1

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.

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA over 1 year ago

FIMS - v0.3.0

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.

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA over 1 year ago

FIMS - 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 (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:

New Contributors

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

Biosphere - Marine Life and Fishery - C++
Published by ChristineStawitz-NOAA over 2 years ago

FIMS - v0.1.0.0

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

Biosphere - Marine Life and Fishery - C++
Published by ChristineStawitz-NOAA almost 3 years ago