NEWS
FIMS 0.9.3
- Reduce verbose FIMS logging and refine messages
- Cleans up integration tests after switching log_devs to random effects
- Revert changes that eliminated compiler warnings because they were
causing tests to fail but not R CMD check
FIMS 0.9.2
- Fixes Rcpp creation of a new Parameter when the input is not valid
FIMS 0.9.1
- Adds vignette on FIMSFrame and data_big
- Adds logging information to fims-demo and updates the logging vignette to be
dynamic instead of relying on a saved image
- Adds a vignette on how to add new C++ modules to FIMS
- Adds WHAM-inspired convergence checks to FIMS models
- Relies on SparseNUTS for Bayesian test
- Refactors FIMSFrame plot method to provide a summary of the data
FIMS 0.9.0
- Adds time-varying weight-at-age
- Adds time-varying selectivity
- Makes recruitment deviations random effects by default when using the wrapper
functions
- Adds a glossary of mathematical symbols to the doxygen documentation
- Brings doxygen to the pkgdown site
- Fixes hidden bug in
dimension_folded_to_tibble() in while loop
- Removes get_log_module
- Removes calculation of uncertainty within the C++ code
- Changed package data name to data_big and added helper data
- Changes
m_*() functions to model_*()
FIMS 0.8.1
- Fixes two bugs in
fit_fims when getting random effect names and not wanting
measurements of uncertainty
- Enhance the documentation by adding a Cheatsheet, updating the README,
increasing information for some functions, added Rcpp training vignette,
adding additional equations to doxygen
FIMS 0.8.0
- Allow for projections based on fixed fishing mortality, catches, or in theory
using priors on any parameter or derived quantity that you want such as
the ratio of current spawning biomass to initial biomass.
- Fixes create_default_Population() to define age and years for log_M
FIMS 0.7.1
- Fixes json output when there are non numeric values, infinity values, and -999
- Allows the output columns to be merged with reshape and dplyr when character
values are combined with strings
- Fixes spawning biomass output in print method to report value
- Fixes get_output() when there is no sdreport with added argument do_sd_report
FIMS 0.7.0
- Turns on the code for model families that allows for more model types in the
future than just the catch-at-age model that is currently implemented through
the use of FisheryModelBase, which is a unified parent class for all model
families. Moved derived quantities (e.g., numbers at age, spawning biomass,
catch at age) from Fleet and Population objects into FisheryModelBase.
Refactored Population and Fleet classes to be trait only objects
- Converts nested list of lists used for model control to a tibble with one line
per parameter that can be un-nested and nested.
- Increased the documentation of FIMS by using formulas in doxygen, building the
doxygen on the NOAA-FIMS github.io site instead of its own web page, writing
more information in the testing README, etc.
- Removes seasonality logic given it was not being used
- Removes date columns in input data in exchange for timing
- Uses {stockplotr} for the figures in the "fims-demo" vignette
FIMS 0.6.3
- Fixes bugs in fims_math.hpp when using TMBad library to use the standard
library functions (exp, log, cos, sqrt, pow) when necessary.
FIMS 0.6.2
- Fixes bug where
unfished_biomass was not initialized.
- Adds TMBad flag to windows Make file.
FIMS 0.6.1
- Fixes FIMS log file where the user was not known on certain operating systems.
FIMS 0.6.0
- Initializes backend code to support model families.
- Returns ungrouped tibble from
get_estimates().
FIMS 0.5.3
- Fix json output to use full stop rather than underscore for names, a bug
introduced in v0.5.0. Also fixes
reshape_tmb_estimates() where the splits
were incorrectly referenced because module_id comes before the label.
FIMS 0.5.2
- Fixes constructor in ParameterVector to error if the size is too small.
FIMS 0.5.1
- Fixes fix-pr-commands.yml permissions and to use the parent workflow.
FIMS 0.5.0
- Implements random effects
- Adds fits tibble to output with
get_fits()
- Switch to TMBad from CppAD
- Checks that length data has the correct dimension in R
- Adds SB to model output
- Adds README files to the C++ code
- Exports logit functions to R
- Adds capabilities in GitHub actions to document
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.
FIMS 0.3.0.1
- 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.
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 nlminb;
- 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.
FIMS 0.2.0.0
- 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
FIMS 0.1.0.0
- Added a
NEWS.md file to track changes to the package.