Release 0.3.0.0

[kellijohnson-NOAA]

What is the feature?

• Version 0.3.0.0

How have you implemented the solution?

• 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.

Does the PR impact any other area of the project, maybe another repo?

• Case studies need updated
• Additional tasks that need to be thought about
  • Remove code for processR in tests
  • Find TODO statements in documentation and add the documentation
  • think about renaming some of the Rcpp functions
  • cli_* needs to be implemented throughout the package
  • fix(fims-demo): Does not use returned object from fit_fims for plots
  • no metadata object found to revise superClass error with sdreport class
  • Add a standalone test (CI-only) for checking the speed of parallel runs
  • fix parallel tests to avoid comparing run time with serial execution

[github-actions]

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Checklist

• The PR is requested to be merged into the appropriate branch (typically main)
• The code is well-designed.
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[codecov]

Codecov Report

Attention: Patch coverage is 62.90076% with 243 lines in your changes missing coverage. Please review.

Project coverage is 65.73%. Comparing base (f0d4e76) to head (a65e05b).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
inst/include/common/def.hpp	8.33%	93 Missing and 6 partials ⚠️
inst/include/utilities/fims_json.hpp	52.94%	55 Missing and 41 partials ⚠️
...lude/population_dynamics/population/population.hpp	92.15%	0 Missing and 16 partials ⚠️
inst/include/population_dynamics/fleet/fleet.hpp	78.94%	0 Missing and 12 partials ⚠️
inst/include/common/fims_vector.hpp	75.00%	4 Missing and 6 partials ⚠️
..._dynamics/selectivity/functors/double_logistic.hpp	63.63%	4 Missing ⚠️
...population_dynamics/maturity/functors/logistic.hpp	66.66%	2 Missing ⚠️
...ulation_dynamics/selectivity/functors/logistic.hpp	75.00%	2 Missing ⚠️
...clude/population_dynamics/growth/functors/ewaa.hpp	75.00%	0 Missing and 1 partial ⚠️
...dynamics/recruitment/functors/sr_beverton_holt.hpp	50.00%	0 Missing and 1 partial ⚠️

❗ There is a different number of reports uploaded between BASE (f0d4e76) and HEAD (a65e05b). Click for more details.

HEAD has 1 upload less than BASE

Flag	BASE (f0d4e76)	HEAD (a65e05b)
	2	1

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #712       +/-   ##
===========================================
- Coverage   78.78%   65.73%   -13.06%     
===========================================
  Files          36       16       -20     
  Lines        1975      715     -1260     
  Branches      141      197       +56     
===========================================
- Hits         1556      470     -1086     
+ Misses        376      160      -216     
- Partials       43       85       +42     

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