NEWS

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FIMS 0.11.0

Bug Fixes

• (CatchAtAge) Build expected length comps from age comp proportions (#1751)
• (devcontainer) Add missing comma
• (fims_likelihood) Use module_name when selecting the profiled parameter (#1774)
• (fimsfit) Name random effects in the sdreport so their standard errors reach get_estimates() (#1773)
• (get_estimates) Adds random effect distribution parameters (#1771)
• (information) Drop density component links
• (interface) Register fleet log_q and maturity parameters in variable_map (#1793)
• (json) Keep whitespace inside strings and decode escapes
• (model) Clear the TMB objective function pointer after each evaluation (#1766)
• (output) Write fleet names and keep infinite values readable (#1770)
• (selectivity) Error on a logit_sel_at_age length that does not fit n_ages
• (setup_default_parameters) Use the geometric plus group for default initial numbers (#1787)
• (test) Update initial values for estimation tests
• (No Category) Docs: fix broken relative URLs in adding-new-module vignette
• (No Category) File paths were too long for windows

Documentation

• (mohns_rho) Fix sign of Mohn's rho in documentation (#1772)
• (No Category) Adds more exploration/explanation to demo

Features

• (growth) Size and growth infrastructure (#1697)
• (selelectivity) Selectivity at age

Performance

• (fit_fims) Skip the derived-quantity covariance in sdreport (#1775)

New Contributors

• @grantdadams made their first contribution in #1771
• @VedantMadane made their first contribution in #1703

Commit Statistics

• 20 commit(s) contributed to the release.
• 38 day(s) passed between the first and last commit.
• 20 commit(s) parsed as conventional.
• 15 linked issue/PR reference(s) detected in commits.
  • #1748 (referenced 3 time(s))
  • #1764 (referenced 2 time(s))
  • #1556 (referenced 1 time(s))
  • #1697 (referenced 1 time(s))
  • #1739 (referenced 1 time(s))
  • #1751 (referenced 1 time(s))
  • #1766 (referenced 1 time(s))
  • #1770 (referenced 1 time(s))
  • #1771 (referenced 1 time(s))
  • #1772 (referenced 1 time(s))
  • #1773 (referenced 1 time(s))
  • #1774 (referenced 1 time(s))
  • #1775 (referenced 1 time(s))
  • #1787 (referenced 1 time(s))
  • #1793 (referenced 1 time(s))
• 53 day(s) passed between releases.

FIMS 0.10.0

• Use setup_default_parameters() to set up a model
• Specify uncertainty using a formula with a distribution and arguments
• Change time to timing in parameter tibble
• Change value to observed in FIMSFrame
• Rename get_timing() to get_run_time()
• Change landings to catch everywhere (R and C++)

FIMS 0.9.4

• Adds likelihood profiles and retrospective diagnostic tools
• Adds priors on derived quantities
• Adds tidy output with yardstick
• Uses .data and .env for dplyr instead of globalVariable()
• Uses translational units to decrease RAM during compile
• Expose proportion_female as a scalar that can be set
• Fixes sanitizing values for JSON
• Fixes naming of phi_0
• Fixes inability to initialize a fleet with index and catch
• Breaking change: "name" to "fleet" in FIMSFrame
• Breaking change: "fleet_name" to "fleet" in output from get_estimates()

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 catch 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.