NEWS

FIMS 0.3.0.0

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.

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