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Recent Releases of FIMS

FIMS - v0.10.0

What's Changed

  • Use setup_default_parameters() to set up a model
  • Specify uncertainty in the input data frame using a formula with a distribution and arguments
  • Change time to timing in parameter tibble
  • Change value to observed in FIMSFrame
  • Rename get_timing() to get_run_time()
  • Change landings to catch everywhere (R and C++)

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.9.4...v0.10.0

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 21 days ago

FIMS - v0.9.4

What's Changed

Bug Fixes

Breaking Changes

  • name is now fleet in FIMSFrame
  • fleet_name is now fleet in FIMSFit

Refactor Changes

New features

New Contributors

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.9.3...v0.9.4

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

FIMS - v0.9.3

What's Changed

  • Reduce verbose FIMS logging and refine messages by @msupernaw
  • Cleans up integration tests after switching log_devs to random effects by @Andrea-Havron-NOAA
  • Revert some changes that eliminated compiler warnings because they were causing tests to fail but not R CMD check

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.9.2...v0.9.3

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 5 months ago

FIMS - v0.9.2

What's Changed

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.9.1...v0.9.2

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 5 months ago

FIMS - v0.9.1

What's Changed

  • Adds vignette on FIMSFrame and data_big
  • Adds logging information to fims-demo and updates the logging vignette to be
    dynamic instead of relying on a saved image
  • Adds a vignette on how to add new C++ modules to FIMS
  • Adds WHAM-inspired convergence checks to FIMS models
  • Relies on SparseNUTS for Bayesian test
  • Refactors FIMSFrame plot method to provide a summary of the data

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.8.1...v0.9.1

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 5 months ago

FIMS - v0.9.0

What's Changed

  • Adds time-varying weight-at-age
  • Adds time-varying selectivity
  • Makes recruitment deviations random effects by default when using the wrapper functions
  • Adds a glossary of mathematical symbols to the doxygen documentation
  • Brings doxygen to the pkgdown site
  • Fixes hidden bug in dimension_folded_to_tibble() in while loop
  • Removes get_log_module
  • Removes calculation of uncertainty within the C++ code
  • Changed package data name to data_big and added helper data
  • Changes m_() functions to model_()

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.8.1...v0.9.0

Thank You

We would like to thank the new and continuing contributors that helped with this release, which includes changes from 25 Pull Requests. Way to go team 💪🏅.

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 6 months ago

FIMS - v0.8.1

What's Changed

  • Two 🐛 were fixed relating to getting the names of the random-effect parameters and not turning off sd reporting.
  • The uncertainty of the length-to-age-conversion matrix is no longer being calculated because it is a fixed input as of right now
  • Lots of documentation was improved and compiler warnings were decreased by making the code more robust

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.8.0...v0.8.1

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 6 months ago

FIMS - v0.8.0

What's Changed

  • Model time series can now include projections
  • Vignette on sparsity with random effects given the parameterization of the model

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.7.1...v0.8.0

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 8 months ago

FIMS - v0.7.1

What's Changed

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.7.0...v0.7.1

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 8 months ago

FIMS - v0.7.0

What's Changed

  • Turns on the code for model families that allows for more model types in the future than just the catch-at-age model that is currently implemented through the use of FisheryModelBase, which is a unified parent class for all model families. Moved derived quantities (e.g., numbers at age, spawning biomass, catch at age) from Fleet and Population objects into FisheryModelBase. Refactored Population and Fleet classes to be trait only objects.
  • Converts nested list of lists used for model control to a tibble with one line per parameter that can be un-nested and nested.
  • Increased the documentation of FIMS by using formulas in doxygen, building the doxygen on the NOAA-FIMS github.io site instead of its own web page, writing more information in the testing README, etc.
  • Removes seasonality logic given it was not being used.
  • Removes date columns in input data in exchange for timing.
  • Uses {stockplotr} for the figures in the "fims-demo" vignette.

Full Changelog: https://github.com/NOAA-FIMS/FIMS/compare/v0.6.3...v0.7.0

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA 9 months ago

FIMS - v0.6.3

Biosphere - Marine Life and Fishery - C++
Published by kellijohnson-NOAA about 1 year 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 about 1 year 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 about 1 year 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 about 1 year 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 about 1 year 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 about 1 year 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 about 1 year 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 over 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 about 3 years ago