- 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()
, andinitialize_*()
; - 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.
- creating the input model specifications with
- 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
(#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
andend_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
- Added a
NEWS.md
file to track changes to the package.