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Recent Releases of FIMS

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 3 months 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 4 months 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 1 year 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 2 years ago