Changelog • FIMS

FIMS 0.4.0

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.

Pluralism in cli was incorrect in FIMSFrame.
Composition modules are initialized using the composition times the uncertainty, which was failing for -999 values because -999 * uncertainty does not equal -999 and was leading to the likelihood being evaluated.

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