[Developer Issue]: M2 Quality control task list #662

kellijohnson-NOAA · 2024-08-07T21:30:16Z

Description

This issue will be a collect all for small tasks that need to be completed for quality control after features are implemented in milestone 2. For example, @rklasky mentioned there are a few spelling mistakes in the code that need cleaned up. Feel free to edit this comment or post more comments below regarding small things that need to be done before our next release.

Tasks

Give feedback

remove estimate_q from the fleet module, as a parameter vector for q needs to be created. Use fleet$log_q[1]$estimated <- TRUE instead
class "sdreport" is defined (with package slot 'FIMS') but no metadata object found to revise superClass information---not imported? Making a copy in package 'FIMS'
rename get_output() to not start with get because that is used in the accessors of S4 objects
Fix output of get_output() if finalize() has not been called, e.g., Invalid request to "get_output". Please call finalize first.[1] "" should not have [1] but it is not clear in the code why it is being printed because the c++ code is "Invalid request to \"get_output()\". Please call finalize() first." (Matthew)
create a check for building the website and calculating code coverage if being merged into a different branch or on every push
Link to doxygen in logging_system vignette instead of having minimal information on Public Attributes (Kelli)
Add Bayesian demo and other distribution tests, make this a Discussion (Kelli)
Review all R functions to identify which should be exposed to users with the @export tag and then group them in the _pkgdown.yml file
Document Rcpp functions with titles, e.g., Rcpp::function("CreateTMBModel", &CreateTMBModel, "Initialize the FIMS/TMB model")
Fix function names throughout to use camel case in the C++.
update initialize_fims() and make sure only length-comp data scenario works (Bai)
remove .vscode folder if we want to and add it to .gitignore (Matthew)
Ensure use :: for all packages other than FIMS, e.g., methods::new() in maturity vignette (Andrea)
Line 196 of rcpp_interface_base.hpp should be changed to if (static_cast<size_t>(pos) == 0 || static_cast<size_t>(pos) > this->storage_m->size()) { from if (pos == 0 || pos > this->storage_m->size()) {
Make documentation in rcpp_interface Full sentences. #691

P3 attribute: low hanging 🍎 kind: documentation theme: documentation
remove commented-out code, e.g., // data_indicator<tmbutils::vector<Type> , Type> keep;
Fix spacing in information.hpp FIMS_INFO_LOG("Random effect size for distribution " + fims::to_string(d->id) + "is: " + fims::to_string(d->x.size())); where it needs a space before is.
remove "TMB" from distribution class names and distribution files.
should be able to remove library(TMB) call from vignettes but this needs to be tested
fix data-raw/data_mile1.R so you can source the file from your working directory, right now it only works if you run it line by line (Bai)
change FIMSFrame functions to all start with get_*() like get_data() (Bai and Kelli)
Fix documentation for set_all_random, e.g., .method("set_all_random", &ParameterVector::set_all_random, "Sets all Parameters within vector as estimable.")
write tests for length (Nathan and Bai)
Edit authors, creators, and contributors in DESCRIPTION (Kelli)
Change clear() to nuke (Matthew)
Remove size_t index_yf = year * population.nfleets + fleet_index; from test_population_Unfished_Initial.cpp clang-tidy recognized it as not being used
Refactor information (Ron and Andrea)
document methods in R/fimsframe.R using @Rdname like how it is done for m_lengthcomp (Meg)
Use %in% in R/fimsframe.R instances of .data[["name"]] == fleet_name (Meg)
in data-raw/data_mile1.R change maindir to main_dir` (Bai)
case studies should be ran every week and main should be checked every week, needs changes to the .github/workflows files (Ian/Jane/Kathryn)
Remove author name, email, and date created from C++ files (Ian/Jane/Kathryn)
Fix spelling of "sucess" to "success" in vignette/fims-demo (Matthew)
Fix spelling of "proirs" to "priors" (Matthew)
Change actions/checkout@v3 to v4 (Ian/Jane/Kathryn)
add call-spell-check.yml from {ghactions4r} into the FIMS GHA workflows (Ian/Jane/Kathryn)
exchange $ for [[""]] in R/distribution_formulas.R for all non-module calls (Kelli)
Add non vignettes/*.Rmd files to .gitignore
In information.hpp the exit(1) command is a bit heavy handed (imho)
In information.hpp valid_model never is used due to the exit(1) command
stop showing the data frames that are available in the vignette
add .gitignore to vignettes to ignore everything but .Rmd files
remove non-essential settings from fims-demo and use documentation or args() to display default settings (Bai)
fix C++ so the number of warnings when compiling is reduced to a minimal number (Matthew)
Options

The text was updated successfully, but these errors were encountered:

k-doering-NOAA · 2024-08-07T21:35:38Z

As a solution for spelling mistakes in the long term, there is a github action that runs the spelling::spell_check_package() in ghactions4r: https://nmfs-fish-tools.github.io/ghactions4r/reference/use_spell_check.html

@Bai-Li-NOAA

Was PR #652 and commit e0fbfb0 but that was based on main and enough has changed that the commit had be redone for dev. There are still some interfaces that are not documented but they can be completed in #662. Thanks to @Bai-Li-NOAA for this commit :) Close #635

…workflows #662 Co-authored-by: Jane Sullivan <[email protected]> Co-authored-by: Kathryn Doering <[email protected]>

…workflows related to #662 Co-authored-by: Jane Sullivan <[email protected]> Co-authored-by: Kathryn Doering <[email protected]>

@Seealso

Performed in the FIMS GHA workflows Fixes the double space was causing roxygen2 to render the file with @Seealso rather than interpreting the @ as a tag. This caused seealso to be needed in the WORDLIST. Changes proirs to priors in c++ documentation related to #662 Co-authored-by: Jane Sullivan <[email protected]> Co-authored-by: Kathryn Doering <[email protected]>

Part of #662

@Seealso

Performed in the FIMS GHA workflows Fixes the double space was causing roxygen2 to render the file with @Seealso rather than interpreting the @ as a tag. This caused seealso to be needed in the WORDLIST. Changes proirs to priors in c++ documentation related to #662 Co-authored-by: Jane Sullivan <[email protected]> Co-authored-by: Kathryn Doering <[email protected]>

Part of #662

Many of the accessors were not documented, also increases the consistency of the documentation. Also fixes fleet subsetting to allow for multiple fleets rather than using ==, where it now uses %in% Part of #662

Use full sentences and multiline comments to document things in the Rcpp interface rather than inline comments. This leads to better roxygen output. I also spaced things by two spaces rather than 4 for consistence but the rest of the code needs to be fixed as well. Part of #662

@brief

* fit to length data using an age-length-conversion matrix. * Adds ParameterVector to allow for time-varying parameters. * Wrapper functions in R to help users set up a model given their data. * Implemented a helper function to get the parameter names throughout the C++ code and population the results with those names. * Adds density functions to set up for random effects R ---- doc(FIMSFrame): Adds documentation to accessors and increased consistency doc(ParameterVector): Adds time-varying example to the vignette that is turned off by default but users can experiment doc: Shares argument documentation across functions doc(fims-demo): Adds example of a model that is built but not fit feat(create_default_*()): Creates default values for FIMS parameters feat(update_parameters()): Updates default values for FIMS parameters feat(initialize_*()): Uses methods::new() to set up FIMS modules feat(FIMSFit): Created FIMSFit as an S4 Class with [create_FIMSFit()] so people can also create a FIMSFit object without having to use [fit_fims()] and so the object returned by [fit_fims()] looks the same no matter if you want the uncertainty calculated or not via `get_sd`. Objects are not added to things to obj, opt, and report and instead they are explicitly returned as a slot in the S4 FIMSFit class feat(estimates): In FIMSFit feat(verbose): Uses cli_inform cli_abort. Users can now set the global verbose level through `options(rlib_message_verbosity = "quiet")` to stop cli::cli_inform() messages from coming through. This allows for the verbose argument to be removed from all functions. And, [is_fims_verbose()] can check internally in functions to see if FIMS is currently verbose. fix(data1): Renamed from data_mile1 and adds length data fix(fims-demo): Updates vignette doi Bai et al. fix(FIMSFrame): Allows for subsetting of multiple fleets with %in% fix(plot.FIMSFrame): Adds y and ... for plot to be properly documented where previously we only had x, which led to scales not being seen as a package that was needed. The methods proposed in #672 was a work around where this commit fixes the problem. fix(Rcpp_Parameter*): Moves to zzz.R because when in operators it was leading to warnings when compiling in R. The movement allows this file to be ran before the others and it does not matter if Rcpp_Parameter or Rcpp_ParameterVector is exported/defined. I also worked on the formatting of those functions as well as combining the documentation rather for similar, i.e., methods. refactor(cli): Updates error message to use cli formatting refactor(DESCRIPTION): Adds packages * Adds purrr, tidyr, tibble, stats * Removes tidyverse * Depends on R 4.1.0 because of the use of the native pipe, which is available in R version 4.1.0. Status-quo dependency was R 4.0. refactor(tests): convert tests to testthat format in test-unit-rcpp-interface-variable-vector.R C++ ---- doc: Remove authors, email from file headers, some cleanup to cpp file header with consistent use of @file, @brief, @details, and @copyright for every file in inst/include and notes. doc(mainpage): Adds mainpage for doxygen as discussed by the documentation group led by @Bai-Li-NOAA in July (notes [here]( https://docs.google.com/document/d/1tPCSSanZ7SHaSE5SMkPoYrZh_lsswe7o5gtEyJmA0DU/edit?tab=t.0#heading=h.enmw68u5r5hm)). doc(Parameter): Fully documents Parameter and ParameterVector matching documentation at the function definition with what is shown in Rcpp methods::show() inside R. doc(pos): Uses pos in position for time-varying so it does not seem like things can only vary with time. feat: add variable_map infrastructure * adds variable map as an object in information.hpp * adds std::vector<uint32_t> key to density_components_base * adds unique ID to VariableVector class and get_id function * resizes key and pass to densities in rcpp_distributions feat: Uses .estimated_m and .is_random_effect_m in interface feat(get_force_scalar): method in fims::Vector to return the first index if the vector is size one. feat(get_parameter_names): Gets parameter names from C++ fix: Sets unique key for all tracked parameter/derived value in Rcpp objects fix(information): add data error checks in information fix(rcpp_interface): add get and set id functions to fleet interface and expose in fix(multinomial_lpmf.hpp): make lpdf_vec to return 0 if data is missing fix(Parameter): Removes estimated_m fix(Makevars): Removes c++17 flag In favor of USE_CXX17 = "yes" and removes -w flag where this fix is known to work on Windows. fix(clear): Removes everything because there was some information from random effects that was not being cleared leading to crashes. Many functions in the C++ code were also changed to CamelCase such as Clear(). Refactored function names to match style of other member functions. clear() procedure creates a new instance of the information singleton object. fix: Removes log_sigma_recruit from the Beverton--Holt stock--recruitment interface because it is now a part of the distribution associated with log_devs fix(logging): Uses macros * Removes old logging * pretty format for output * added format string for json * created a logging vignette * Adds information about DFIMS_DEBUG information * Adds throw on error fix: Updates name of ParameterVector id to id_m fix: Collapses methods using S4 Group Generic Functions fix: Defines methods for Ops, Math, and Summary fix: Updates parameter min/max default values refactor(model.hpp): Loops over all density modules to sum up joint negative log-likelihoods refactor: Adds i=0 in for loops because R CMD check was complaining about significant warnings in compiling the c++ code because i was not initialized. refactor(information): Improves readability refactor: Uses C++ 17 refactor: Renames SIMULATE_F to FIMS_SIMULATE_F refactor: Renames REPORT_F to FIMS_REPORT_F GitHub ---- chore: change actions/checkout@v3 to v4 feat: Adds call-spell-check.yml from {ghactions4r} to spellcheck with WORDLIST fix: Adds .json to .gitignore fix: Adds .vscode to .gitignore fix: Removes parallel tests because they were not helpful fix: revert sim_num to 100 to simulate 100 sets of test data (see tests/testthat/fixtures/simulate-integration-test-data.R) TODO: ---- * Remove code for processR in tests * Find TODO statements in documentation and add the documentation * think about renaming some of the Rcpp functions * cli_* needs to be implemented throughout the package * fix(fims-demo): Does not use returned object from fit_fims for plots * no metadata object found to revise superClass error with sdreport class * Add a standalone test (CI-only) for checking the speed of parallel runs * fix parallel tests to avoid comparing run time with serial execution Co-authored-by: Andrea-Havron-NOAA <[email protected]> Co-authored-by: Bai-Li-NOAA <[email protected]> Co-authored-by: ChristineStawitz-NOAA <[email protected]> Co-authored-by: cmlegault <[email protected]> Co-authored-by: Cole-Monnahan-NOAA <[email protected]> Co-authored-by: JaneSullivan-NOAA <[email protected]> Co-authored-by: iantaylor-NOAA <[email protected]> Co-authored-by: k-doering-NOAA <[email protected]> Co-authored-by: kellijohnson-NOAA <[email protected]> Co-authored-by: KyleShertzer-NOAA <[email protected]> Co-authored-by: msupernaw <[email protected]> Co-authored-by: nathanvaughan-NOAA <[email protected]> Co-authored-by: rklasky <[email protected]> Part of #170: refactor distributions_base Part of #388 Part of #573: add normal_lpdf Part of #581: add lognormal_lpdf Part of #585: add multinomial_lpmf Part of #586 Part of #630 Part of #644 Part of #645 Part of #646 Part of #662 Part of #671 Part of #695 Part of #702 Close #672 Close #690

@brief

* 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. R ---- doc(FIMSFrame): Adds documentation to accessors and increased consistency doc(ParameterVector): Adds time-varying example to the vignette that is turned off by default but users can experiment doc(fims-demo): Adds example of a model that is built but not fit doc: Shares argument documentation across functions feat(create_default_*()): Creates default values for FIMS parameters feat(update_parameters()): Updates default values for FIMS parameters feat(initialize_*()): Uses methods::new() to set up FIMS modules feat(FIMSFit): Created FIMSFit as an S4 Class with [create_FIMSFit()] so people can also create a FIMSFit object without having to use [fit_fims()] and so the object returned by [fit_fims()] looks the same no matter if you want the uncertainty calculated or not via `get_sd`. Objects are not added to things to obj, opt, and report and instead they are explicitly returned as a slot in the S4 FIMSFit class feat(estimates): In FIMSFit feat(verbose): Uses cli_inform cli_abort. Users can now set the global verbose level through `options(rlib_message_verbosity = "quiet")` to stop cli::cli_inform() messages from coming through. This allows for the verbose argument to be removed from all functions. And, [is_fims_verbose()] can check internally in functions to see if FIMS is currently verbose. fix(data1): Renamed from data_mile1 and adds length data fix(fims-demo): Updates vignette doi Bai et al. fix(FIMSFrame): Allows for subsetting of multiple fleets with %in% fix(plot.FIMSFrame): Adds y and ... for plot to be properly documented where previously we only had x, which led to scales not being seen as a package that was needed. The methods proposed in #672 was a work around where this commit fixes the problem. fix(Rcpp_Parameter*): Moves to zzz.R because when in operators it was leading to warnings when compiling in R. The movement allows this file to be ran before the others and it does not matter if Rcpp_Parameter or Rcpp_ParameterVector is exported/defined. I also worked on the formatting of those functions as well as combining the documentation rather for similar, i.e., methods. refactor(cli): Updates error message to use cli formatting refactor(DESCRIPTION): Adds packages * Adds purrr, tidyr, tibble, stats * Removes tidyverse * Depends on R 4.1.0 because of the use of the native pipe, which is available in R version 4.1.0. Status-quo dependency was R 4.0. refactor(tests): convert tests to testthat format in test-unit-rcpp-interface-variable-vector.R C++ ---- doc: Remove authors, email from file headers, some cleanup to cpp file header with consistent use of @file, @brief, @details, and @copyright for every file in inst/include and notes. doc(mainpage): Adds mainpage for doxygen as discussed by the documentation group led by @Bai-Li-NOAA in July (notes [here]( https://docs.google.com/document/d/1tPCSSanZ7SHaSE5SMkPoYrZh_lsswe7o5gtEyJmA0DU/edit?tab=t.0#heading=h.enmw68u5r5hm)). doc(Parameter): Fully documents Parameter and ParameterVector matching documentation at the function definition with what is shown in Rcpp methods::show() inside R. doc(pos): Uses pos in position for time-varying so it does not seem like things can only vary with time. feat: add variable_map infrastructure * adds variable map as an object in information.hpp * adds std::vector<uint32_t> key to density_components_base * adds unique ID to VariableVector class and get_id function * resizes key and pass to densities in rcpp_distributions feat: Uses .estimated_m and .is_random_effect_m in interface feat(get_force_scalar): method in fims::Vector to return the first index if the vector is size one. feat(get_parameter_names): Gets parameter names from C++ fix: Sets unique key for all tracked parameter/derived value in Rcpp objects fix(information): add data error checks in information fix(rcpp_interface): add get and set id functions to fleet interface fix(multinomial_lpmf.hpp): make lpdf_vec to return 0 if data is missing fix(Parameter): Removes estimated_m fix(Makevars): Removes c++17 flag In favor of USE_CXX17 = "yes" and removes -w flag where this fix is known to work on Windows. fix(clear): Removes everything because there was some information from random effects that was not being cleared leading to crashes. Many functions in the C++ code were also changed to CamelCase such as Clear(). Refactored function names to match style of other member functions. clear() procedure creates a new instance of the information singleton object. fix: Removes log_sigma_recruit from the Beverton--Holt stock--recruitment interface because it is now a part of the distribution associated with log_devs fix(logging): Uses macros * Removes old logging * pretty format for output * added format string for json * created a logging vignette * Adds information about DFIMS_DEBUG information * Adds throw on error fix: Collapses methods using S4 Group Generic Functions fix: Defines methods for Ops, Math, and Summary fix: Updates parameter min/max default values refactor(model.hpp): Loops over all density modules to sum up joint negative log-likelihoods refactor: Adds i=0 in for loops because R CMD check was complaining about significant warnings in compiling the c++ code because i was not initialized. refactor(information): Improves readability refactor: Uses C++ 17 refactor: Renames SIMULATE_F to FIMS_SIMULATE_F refactor: Renames REPORT_F to FIMS_REPORT_F GitHub ---- chore: change actions/checkout@v3 to v4 feat: Adds call-spell-check.yml from {ghactions4r} to spellcheck with WORDLIST fix: Adds .json to .gitignore fix: Adds .vscode to .gitignore fix: Removes parallel tests because they were not helpful fix: revert sim_num to 100 to simulate 100 sets of test data (see tests/testthat/fixtures/simulate-integration-test-data.R) TODO: ---- * Remove code for processR in tests * Find TODO statements in documentation and add the documentation * think about renaming some of the Rcpp functions * cli_* needs to be implemented throughout the package * fix(fims-demo): Does not use returned object from fit_fims for plots * no metadata object found to revise superClass error with sdreport class * Add a standalone test (CI-only) for checking the speed of parallel runs * fix parallel tests to avoid comparing run time with serial execution Co-authored-by: Andrea-Havron-NOAA <[email protected]> Co-authored-by: Bai-Li-NOAA <[email protected]> Co-authored-by: ChristineStawitz-NOAA <[email protected]> Co-authored-by: cmlegault <[email protected]> Co-authored-by: Cole-Monnahan-NOAA <[email protected]> Co-authored-by: JaneSullivan-NOAA <[email protected]> Co-authored-by: iantaylor-NOAA <[email protected]> Co-authored-by: k-doering-NOAA <[email protected]> Co-authored-by: kellijohnson-NOAA <[email protected]> Co-authored-by: KyleShertzer-NOAA <[email protected]> Co-authored-by: msupernaw <[email protected]> Co-authored-by: nathanvaughan-NOAA <[email protected]> Co-authored-by: rklasky <[email protected]> Part of #170: refactor distributions_base Part of #388 Part of #573: add normal_lpdf Part of #581: add lognormal_lpdf Part of #585: add multinomial_lpmf Part of #586 Part of #630 Part of #644 Part of #645 Part of #646 Part of #662 Part of #671 Part of #695 Part of #702 Close #672 Close #690

@brief

* 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. R ---- doc(FIMSFrame): Adds documentation to accessors and increased consistency doc(ParameterVector): Adds time-varying example to the vignette that is turned off by default but users can experiment doc(fims-demo): Adds example of a model that is built but not fit doc: Shares argument documentation across functions feat(create_default_*()): Creates default values for FIMS parameters feat(update_parameters()): Updates default values for FIMS parameters feat(initialize_*()): Uses methods::new() to set up FIMS modules feat(FIMSFit): Created FIMSFit as an S4 Class with [create_FIMSFit()] so people can also create a FIMSFit object without having to use [fit_fims()] and so the object returned by [fit_fims()] looks the same no matter if you want the uncertainty calculated or not via `get_sd`. Objects are not added to things to obj, opt, and report and instead they are explicitly returned as a slot in the S4 FIMSFit class feat(estimates): In FIMSFit feat(verbose): Uses cli_inform cli_abort. Users can now set the global verbose level through `options(rlib_message_verbosity = "quiet")` to stop cli::cli_inform() messages from coming through. This allows for the verbose argument to be removed from all functions. And, [is_fims_verbose()] can check internally in functions to see if FIMS is currently verbose. fix(data1): Renamed from data_mile1 and adds length data fix(fims-demo): Updates vignette doi Bai et al. fix(FIMSFrame): Allows for subsetting of multiple fleets with %in% fix(plot.FIMSFrame): Adds y and ... for plot to be properly documented where previously we only had x, which led to scales not being seen as a package that was needed. The methods proposed in #672 was a work around where this commit fixes the problem. fix(Rcpp_Parameter*): Moves to zzz.R because when in operators it was leading to warnings when compiling in R. The movement allows this file to be ran before the others and it does not matter if Rcpp_Parameter or Rcpp_ParameterVector is exported/defined. I also worked on the formatting of those functions as well as combining the documentation rather for similar, i.e., methods. refactor(cli): Updates error message to use cli formatting refactor(DESCRIPTION): Adds packages * Adds purrr, tidyr, tibble, stats * Removes tidyverse * Depends on R 4.1.0 because of the use of the native pipe, which is available in R version 4.1.0. Status-quo dependency was R 4.0. refactor(tests): convert tests to testthat format in test-unit-rcpp-interface-variable-vector.R C++ ---- doc: Remove authors, email from file headers, some cleanup to cpp file header with consistent use of @file, @brief, @details, and @copyright for every file in inst/include and notes. doc(mainpage): Adds mainpage for doxygen as discussed by the documentation group led by @Bai-Li-NOAA in July (notes [here]( https://docs.google.com/document/d/1tPCSSanZ7SHaSE5SMkPoYrZh_lsswe7o5gtEyJmA0DU/edit?tab=t.0#heading=h.enmw68u5r5hm)). doc(Parameter): Fully documents Parameter and ParameterVector matching documentation at the function definition with what is shown in Rcpp methods::show() inside R. doc(pos): Uses pos in position for time-varying so it does not seem like things can only vary with time. feat: add variable_map infrastructure * adds variable map as an object in information.hpp * adds std::vector<uint32_t> key to density_components_base * adds unique ID to VariableVector class and get_id function * resizes key and pass to densities in rcpp_distributions feat: Uses .estimated_m and .is_random_effect_m in interface feat(get_force_scalar): method in fims::Vector to return the first index if the vector is size one. feat(get_parameter_names): Gets parameter names from C++ fix: Sets unique key for all tracked parameter/derived value in Rcpp objects fix(information): add data error checks in information fix(rcpp_interface): add get and set id functions to fleet interface fix(multinomial_lpmf.hpp): make lpdf_vec to return 0 if data is missing fix(Parameter): Removes estimated_m fix(Makevars): Removes c++17 flag In favor of USE_CXX17 = "yes" and removes -w flag where this fix is known to work on Windows. fix(clear): Removes everything because there was some information from random effects that was not being cleared leading to crashes. Many functions in the C++ code were also changed to CamelCase such as Clear(). Refactored function names to match style of other member functions. clear() procedure creates a new instance of the information singleton object. fix: Removes log_sigma_recruit from the Beverton--Holt stock--recruitment interface because it is now a part of the distribution associated with log_devs fix(logging): Uses macros * Removes old logging * pretty format for output * added format string for json * created a logging vignette * Adds information about DFIMS_DEBUG information * Adds throw on error fix: Collapses methods using S4 Group Generic Functions fix: Defines methods for Ops, Math, and Summary fix: Updates parameter min/max default values refactor(model.hpp): Loops over all density modules to sum up joint negative log-likelihoods refactor: Adds i=0 in for loops because R CMD check was complaining about significant warnings in compiling the c++ code because i was not initialized. refactor(information): Improves readability refactor: Uses C++ 17 refactor: Renames SIMULATE_F to FIMS_SIMULATE_F refactor: Renames REPORT_F to FIMS_REPORT_F GitHub ---- chore: change actions/checkout@v3 to v4 feat: Adds call-spell-check.yml from {ghactions4r} to spellcheck with WORDLIST fix: Adds .json to .gitignore fix: Adds .vscode to .gitignore fix: Removes parallel tests because they were not helpful fix: revert sim_num to 100 to simulate 100 sets of test data (see tests/testthat/fixtures/simulate-integration-test-data.R) TODO: ---- * Remove code for processR in tests * Find TODO statements in documentation and add the documentation * think about renaming some of the Rcpp functions * cli_* needs to be implemented throughout the package * fix(fims-demo): Does not use returned object from fit_fims for plots * no metadata object found to revise superClass error with sdreport class * Add a standalone test (CI-only) for checking the speed of parallel runs * fix parallel tests to avoid comparing run time with serial execution Co-authored-by: Andrea-Havron-NOAA <[email protected]> Co-authored-by: Bai-Li-NOAA <[email protected]> Co-authored-by: ChristineStawitz-NOAA <[email protected]> Co-authored-by: cmlegault <[email protected]> Co-authored-by: Cole-Monnahan-NOAA <[email protected]> Co-authored-by: JaneSullivan-NOAA <[email protected]> Co-authored-by: iantaylor-NOAA <[email protected]> Co-authored-by: k-doering-NOAA <[email protected]> Co-authored-by: kellijohnson-NOAA <[email protected]> Co-authored-by: KyleShertzer-NOAA <[email protected]> Co-authored-by: msupernaw <[email protected]> Co-authored-by: nathanvaughan-NOAA <[email protected]> Co-authored-by: rklasky <[email protected]> Part of #170: refactor distributions_base Part of #388 Part of #573: add normal_lpdf Part of #581: add lognormal_lpdf Part of #585: add multinomial_lpmf Part of #586 Part of #630 Part of #644 Part of #645 Part of #646 Part of #662 Part of #671 Part of #695 Part of #702 Close #672 Close #690

@brief

* 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. R ---- doc(FIMSFrame): Adds documentation to accessors and increased consistency doc(ParameterVector): Adds time-varying example to the vignette that is turned off by default but users can experiment doc(fims-demo): Adds example of a model that is built but not fit doc: Shares argument documentation across functions feat(create_default_*()): Creates default values for FIMS parameters feat(update_parameters()): Updates default values for FIMS parameters feat(initialize_*()): Uses methods::new() to set up FIMS modules feat(FIMSFit): Created FIMSFit as an S4 Class with [create_FIMSFit()] so people can also create a FIMSFit object without having to use [fit_fims()] and so the object returned by [fit_fims()] looks the same no matter if you want the uncertainty calculated or not via `get_sd`. Objects are not added to things to obj, opt, and report and instead they are explicitly returned as a slot in the S4 FIMSFit class feat(estimates): In FIMSFit feat(verbose): Uses cli_inform cli_abort. Users can now set the global verbose level through `options(rlib_message_verbosity = "quiet")` to stop cli::cli_inform() messages from coming through. This allows for the verbose argument to be removed from all functions. And, [is_fims_verbose()] can check internally in functions to see if FIMS is currently verbose. fix(data1): Renamed from data_mile1 and adds length data fix(fims-demo): Updates vignette doi Bai et al. fix(FIMSFrame): Allows for subsetting of multiple fleets with %in% fix(plot.FIMSFrame): Adds y and ... for plot to be properly documented where previously we only had x, which led to scales not being seen as a package that was needed. The methods proposed in #672 was a work around where this commit fixes the problem. fix(Rcpp_Parameter*): Moves to zzz.R because when in operators it was leading to warnings when compiling in R. The movement allows this file to be ran before the others and it does not matter if Rcpp_Parameter or Rcpp_ParameterVector is exported/defined. I also worked on the formatting of those functions as well as combining the documentation rather for similar, i.e., methods. refactor(cli): Updates error message to use cli formatting refactor(DESCRIPTION): Adds packages * Adds purrr, tidyr, tibble, stats * Removes tidyverse * Depends on R 4.1.0 because of the use of the native pipe, which is available in R version 4.1.0. Status-quo dependency was R 4.0. refactor(tests): convert tests to testthat format in test-unit-rcpp-interface-variable-vector.R C++ ---- doc: Remove authors, email from file headers, some cleanup to cpp file header with consistent use of @file, @brief, @details, and @copyright for every file in inst/include and notes. doc(mainpage): Adds mainpage for doxygen as discussed by the documentation group led by @Bai-Li-NOAA in July (notes [here]( https://docs.google.com/document/d/1tPCSSanZ7SHaSE5SMkPoYrZh_lsswe7o5gtEyJmA0DU/edit?tab=t.0#heading=h.enmw68u5r5hm)). doc(Parameter): Fully documents Parameter and ParameterVector matching documentation at the function definition with what is shown in Rcpp methods::show() inside R. doc(pos): Uses pos in position for time-varying so it does not seem like things can only vary with time. feat: add variable_map infrastructure * adds variable map as an object in information.hpp * adds std::vector<uint32_t> key to density_components_base * adds unique ID to VariableVector class and get_id function * resizes key and pass to densities in rcpp_distributions feat: Uses .estimated_m and .is_random_effect_m in interface feat(get_force_scalar): method in fims::Vector to return the first index if the vector is size one. feat(get_parameter_names): Gets parameter names from C++ fix: Sets unique key for all tracked parameter/derived value in Rcpp objects fix(information): add data error checks in information fix(rcpp_interface): add get and set id functions to fleet interface fix(multinomial_lpmf.hpp): make lpdf_vec to return 0 if data is missing fix(Parameter): Removes estimated_m fix(Makevars): Removes c++17 flag In favor of USE_CXX17 = "yes" and removes -w flag where this fix is known to work on Windows. fix(clear): Removes everything because there was some information from random effects that was not being cleared leading to crashes. Many functions in the C++ code were also changed to CamelCase such as Clear(). Refactored function names to match style of other member functions. clear() procedure creates a new instance of the information singleton object. fix: Removes log_sigma_recruit from the Beverton--Holt stock--recruitment interface because it is now a part of the distribution associated with log_devs fix(logging): Uses macros * Removes old logging * pretty format for output * added format string for json * created a logging vignette * Adds information about DFIMS_DEBUG information * Adds throw on error fix: Collapses methods using S4 Group Generic Functions fix: Defines methods for Ops, Math, and Summary fix: Updates parameter min/max default values refactor(model.hpp): Loops over all density modules to sum up joint negative log-likelihoods refactor: Adds i=0 in for loops because R CMD check was complaining about significant warnings in compiling the c++ code because i was not initialized. refactor(information): Improves readability refactor: Uses C++ 17 refactor: Renames SIMULATE_F to FIMS_SIMULATE_F refactor: Renames REPORT_F to FIMS_REPORT_F GitHub ---- chore: change actions/checkout@v3 to v4 feat: Adds call-spell-check.yml from {ghactions4r} to spellcheck with WORDLIST fix: Adds .json to .gitignore fix: Adds .vscode to .gitignore fix: Removes parallel tests because they were not helpful fix: revert sim_num to 100 to simulate 100 sets of test data (see tests/testthat/fixtures/simulate-integration-test-data.R) TODO: ---- * Remove code for processR in tests * Find TODO statements in documentation and add the documentation * think about renaming some of the Rcpp functions * cli_* needs to be implemented throughout the package * fix(fims-demo): Does not use returned object from fit_fims for plots * no metadata object found to revise superClass error with sdreport class * Add a standalone test (CI-only) for checking the speed of parallel runs * fix parallel tests to avoid comparing run time with serial execution Co-authored-by: Andrea-Havron-NOAA <[email protected]> Co-authored-by: Bai-Li-NOAA <[email protected]> Co-authored-by: ChristineStawitz-NOAA <[email protected]> Co-authored-by: cmlegault <[email protected]> Co-authored-by: Cole-Monnahan-NOAA <[email protected]> Co-authored-by: JaneSullivan-NOAA <[email protected]> Co-authored-by: iantaylor-NOAA <[email protected]> Co-authored-by: k-doering-NOAA <[email protected]> Co-authored-by: kellijohnson-NOAA <[email protected]> Co-authored-by: KyleShertzer-NOAA <[email protected]> Co-authored-by: msupernaw <[email protected]> Co-authored-by: nathanvaughan-NOAA <[email protected]> Co-authored-by: rklasky <[email protected]> Part of #170: refactor distributions_base Part of #388 Part of #573: add normal_lpdf Part of #581: add lognormal_lpdf Part of #585: add multinomial_lpmf Part of #586 Part of #630 Part of #644 Part of #645 Part of #646 Part of #662 Part of #671 Part of #695 Part of #702 Close #672 Close #690

@brief

* 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. R ---- doc(FIMSFrame): Adds documentation to accessors and increased consistency doc(ParameterVector): Adds time-varying example to the vignette that is turned off by default but users can experiment doc(fims-demo): Adds example of a model that is built but not fit doc: Shares argument documentation across functions feat(create_default_*()): Creates default values for FIMS parameters feat(update_parameters()): Updates default values for FIMS parameters feat(initialize_*()): Uses methods::new() to set up FIMS modules feat(FIMSFit): Created FIMSFit as an S4 Class with [create_FIMSFit()] so people can also create a FIMSFit object without having to use [fit_fims()] and so the object returned by [fit_fims()] looks the same no matter if you want the uncertainty calculated or not via `get_sd`. Objects are not added to things to obj, opt, and report and instead they are explicitly returned as a slot in the S4 FIMSFit class feat(estimates): In FIMSFit feat(verbose): Uses cli_inform cli_abort. Users can now set the global verbose level through `options(rlib_message_verbosity = "quiet")` to stop cli::cli_inform() messages from coming through. This allows for the verbose argument to be removed from all functions. And, [is_fims_verbose()] can check internally in functions to see if FIMS is currently verbose. fix(data1): Renamed from data_mile1 and adds length data fix(fims-demo): Updates vignette doi Bai et al. fix(FIMSFrame): Allows for subsetting of multiple fleets with %in% fix(plot.FIMSFrame): Adds y and ... for plot to be properly documented where previously we only had x, which led to scales not being seen as a package that was needed. The methods proposed in #672 was a work around where this commit fixes the problem. fix(Rcpp_Parameter*): Moves to zzz.R because when in operators it was leading to warnings when compiling in R. The movement allows this file to be ran before the others and it does not matter if Rcpp_Parameter or Rcpp_ParameterVector is exported/defined. I also worked on the formatting of those functions as well as combining the documentation rather for similar, i.e., methods. refactor(cli): Updates error message to use cli formatting refactor(DESCRIPTION): Adds packages * Adds purrr, tidyr, tibble, stats * Removes tidyverse * Depends on R 4.1.0 because of the use of the native pipe, which is available in R version 4.1.0. Status-quo dependency was R 4.0. refactor(tests): convert tests to testthat format in test-unit-rcpp-interface-variable-vector.R C++ ---- doc: Remove authors, email from file headers, some cleanup to cpp file header with consistent use of @file, @brief, @details, and @copyright for every file in inst/include and notes. doc(mainpage): Adds mainpage for doxygen as discussed by the documentation group led by @Bai-Li-NOAA in July (notes [here]( https://docs.google.com/document/d/1tPCSSanZ7SHaSE5SMkPoYrZh_lsswe7o5gtEyJmA0DU/edit?tab=t.0#heading=h.enmw68u5r5hm)). doc(Parameter): Fully documents Parameter and ParameterVector matching documentation at the function definition with what is shown in Rcpp methods::show() inside R. doc(pos): Uses pos in position for time-varying so it does not seem like things can only vary with time. feat: add variable_map infrastructure * adds variable map as an object in information.hpp * adds std::vector<uint32_t> key to density_components_base * adds unique ID to VariableVector class and get_id function * resizes key and pass to densities in rcpp_distributions feat: Uses .estimated_m and .is_random_effect_m in interface feat(get_force_scalar): method in fims::Vector to return the first index if the vector is size one. feat(get_parameter_names): Gets parameter names from C++ fix: Sets unique key for all tracked parameter/derived value in Rcpp objects fix(information): add data error checks in information fix(rcpp_interface): add get and set id functions to fleet interface fix(multinomial_lpmf.hpp): make lpdf_vec to return 0 if data is missing fix(Parameter): Removes estimated_m fix(Makevars): Removes c++17 flag In favor of USE_CXX17 = "yes" and removes -w flag where this fix is known to work on Windows. fix(clear): Removes everything because there was some information from random effects that was not being cleared leading to crashes. Many functions in the C++ code were also changed to CamelCase such as Clear(). Refactored function names to match style of other member functions. clear() procedure creates a new instance of the information singleton object. fix: Removes log_sigma_recruit from the Beverton--Holt stock--recruitment interface because it is now a part of the distribution associated with log_devs fix(logging): Uses macros * Removes old logging * pretty format for output * added format string for json * created a logging vignette * Adds information about DFIMS_DEBUG information * Adds throw on error fix: Collapses methods using S4 Group Generic Functions fix: Defines methods for Ops, Math, and Summary fix: Updates parameter min/max default values refactor(model.hpp): Loops over all density modules to sum up joint negative log-likelihoods refactor: Adds i=0 in for loops because R CMD check was complaining about significant warnings in compiling the c++ code because i was not initialized. refactor(information): Improves readability refactor: Uses C++ 17 refactor: Renames SIMULATE_F to FIMS_SIMULATE_F refactor: Renames REPORT_F to FIMS_REPORT_F GitHub ---- chore: change actions/checkout@v3 to v4 feat: Adds call-spell-check.yml from {ghactions4r} to spellcheck with WORDLIST fix: Adds .json to .gitignore fix: Adds .vscode to .gitignore fix: Removes parallel tests because they were not helpful fix: revert sim_num to 100 to simulate 100 sets of test data (see tests/testthat/fixtures/simulate-integration-test-data.R) TODO: ---- * Remove code for processR in tests * Find TODO statements in documentation and add the documentation * think about renaming some of the Rcpp functions * cli_* needs to be implemented throughout the package * fix(fims-demo): Does not use returned object from fit_fims for plots * no metadata object found to revise superClass error with sdreport class * Add a standalone test (CI-only) for checking the speed of parallel runs * fix parallel tests to avoid comparing run time with serial execution Co-authored-by: Andrea-Havron-NOAA <[email protected]> Co-authored-by: Bai-Li-NOAA <[email protected]> Co-authored-by: ChristineStawitz-NOAA <[email protected]> Co-authored-by: cmlegault <[email protected]> Co-authored-by: Cole-Monnahan-NOAA <[email protected]> Co-authored-by: JaneSullivan-NOAA <[email protected]> Co-authored-by: iantaylor-NOAA <[email protected]> Co-authored-by: k-doering-NOAA <[email protected]> Co-authored-by: kellijohnson-NOAA <[email protected]> Co-authored-by: KyleShertzer-NOAA <[email protected]> Co-authored-by: msupernaw <[email protected]> Co-authored-by: nathanvaughan-NOAA <[email protected]> Co-authored-by: rklasky <[email protected]> Part of #170: refactor distributions_base Part of #388 Part of #573: add normal_lpdf Part of #581: add lognormal_lpdf Part of #585: add multinomial_lpmf Part of #586 Part of #630 Part of #644 Part of #645 Part of #646 Part of #662 Part of #671 Part of #695 Part of #702 Close #672 Close #690

@brief

* 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. R ---- doc(FIMSFrame): Adds documentation to accessors and increased consistency doc(ParameterVector): Adds time-varying example to the vignette that is turned off by default but users can experiment doc(fims-demo): Adds example of a model that is built but not fit doc: Shares argument documentation across functions feat(create_default_*()): Creates default values for FIMS parameters feat(update_parameters()): Updates default values for FIMS parameters feat(initialize_*()): Uses methods::new() to set up FIMS modules feat(FIMSFit): Created FIMSFit as an S4 Class with [create_FIMSFit()] so people can also create a FIMSFit object without having to use [fit_fims()] and so the object returned by [fit_fims()] looks the same no matter if you want the uncertainty calculated or not via `get_sd`. Objects are not added to things to obj, opt, and report and instead they are explicitly returned as a slot in the S4 FIMSFit class feat(estimates): In FIMSFit feat(verbose): Uses cli_inform cli_abort. Users can now set the global verbose level through `options(rlib_message_verbosity = "quiet")` to stop cli::cli_inform() messages from coming through. This allows for the verbose argument to be removed from all functions. And, [is_fims_verbose()] can check internally in functions to see if FIMS is currently verbose. fix(data1): Renamed from data_mile1 and adds length data fix(fims-demo): Updates vignette doi Bai et al. fix(FIMSFrame): Allows for subsetting of multiple fleets with %in% fix(plot.FIMSFrame): Adds y and ... for plot to be properly documented where previously we only had x, which led to scales not being seen as a package that was needed. The methods proposed in #672 was a work around where this commit fixes the problem. fix(Rcpp_Parameter*): Moves to zzz.R because when in operators it was leading to warnings when compiling in R. The movement allows this file to be ran before the others and it does not matter if Rcpp_Parameter or Rcpp_ParameterVector is exported/defined. I also worked on the formatting of those functions as well as combining the documentation rather for similar, i.e., methods. refactor(cli): Updates error message to use cli formatting refactor(DESCRIPTION): Adds packages * Adds purrr, tidyr, tibble, stats * Removes tidyverse * Depends on R 4.1.0 because of the use of the native pipe, which is available in R version 4.1.0. Status-quo dependency was R 4.0. refactor(tests): convert tests to testthat format in test-unit-rcpp-interface-variable-vector.R C++ ---- doc: Remove authors, email from file headers, some cleanup to cpp file header with consistent use of @file, @brief, @details, and @copyright for every file in inst/include and notes. doc(mainpage): Adds mainpage for doxygen as discussed by the documentation group led by @Bai-Li-NOAA in July (notes [here]( https://docs.google.com/document/d/1tPCSSanZ7SHaSE5SMkPoYrZh_lsswe7o5gtEyJmA0DU/edit?tab=t.0#heading=h.enmw68u5r5hm)). doc(Parameter): Fully documents Parameter and ParameterVector matching documentation at the function definition with what is shown in Rcpp methods::show() inside R. doc(pos): Uses pos in position for time-varying so it does not seem like things can only vary with time. feat: add variable_map infrastructure * adds variable map as an object in information.hpp * adds std::vector<uint32_t> key to density_components_base * adds unique ID to VariableVector class and get_id function * resizes key and pass to densities in rcpp_distributions feat: Uses .estimated_m and .is_random_effect_m in interface feat(get_force_scalar): method in fims::Vector to return the first index if the vector is size one. feat(get_parameter_names): Gets parameter names from C++ fix: Sets unique key for all tracked parameter/derived value in Rcpp objects fix(information): add data error checks in information fix(rcpp_interface): add get and set id functions to fleet interface fix(multinomial_lpmf.hpp): make lpdf_vec to return 0 if data is missing fix(Parameter): Removes estimated_m fix(Makevars): Removes c++17 flag In favor of USE_CXX17 = "yes" and removes -w flag where this fix is known to work on Windows. fix(clear): Removes everything because there was some information from random effects that was not being cleared leading to crashes. Many functions in the C++ code were also changed to CamelCase such as Clear(). Refactored function names to match style of other member functions. clear() procedure creates a new instance of the information singleton object. fix: Removes log_sigma_recruit from the Beverton--Holt stock--recruitment interface because it is now a part of the distribution associated with log_devs fix(logging): Uses macros * Removes old logging * pretty format for output * added format string for json * created a logging vignette * Adds information about DFIMS_DEBUG information * Adds throw on error fix: Collapses methods using S4 Group Generic Functions fix: Defines methods for Ops, Math, and Summary fix: Updates parameter min/max default values refactor(model.hpp): Loops over all density modules to sum up joint negative log-likelihoods refactor: Adds i=0 in for loops because R CMD check was complaining about significant warnings in compiling the c++ code because i was not initialized. refactor(information): Improves readability refactor: Uses C++ 17 refactor: Renames SIMULATE_F to FIMS_SIMULATE_F refactor: Renames REPORT_F to FIMS_REPORT_F GitHub ---- chore: change actions/checkout@v3 to v4 feat: Adds call-spell-check.yml from {ghactions4r} to spellcheck with WORDLIST fix: Adds .json to .gitignore fix: Adds .vscode to .gitignore fix: Removes parallel tests because they were not helpful fix: revert sim_num to 100 to simulate 100 sets of test data (see tests/testthat/fixtures/simulate-integration-test-data.R) TODO: ---- * Remove code for processR in tests * Find TODO statements in documentation and add the documentation * think about renaming some of the Rcpp functions * cli_* needs to be implemented throughout the package * fix(fims-demo): Does not use returned object from fit_fims for plots * no metadata object found to revise superClass error with sdreport class * Add a standalone test (CI-only) for checking the speed of parallel runs * fix parallel tests to avoid comparing run time with serial execution Co-authored-by: Andrea-Havron-NOAA <[email protected]> Co-authored-by: Bai-Li-NOAA <[email protected]> Co-authored-by: ChristineStawitz-NOAA <[email protected]> Co-authored-by: cmlegault <[email protected]> Co-authored-by: Cole-Monnahan-NOAA <[email protected]> Co-authored-by: JaneSullivan-NOAA <[email protected]> Co-authored-by: iantaylor-NOAA <[email protected]> Co-authored-by: k-doering-NOAA <[email protected]> Co-authored-by: kellijohnson-NOAA <[email protected]> Co-authored-by: KyleShertzer-NOAA <[email protected]> Co-authored-by: msupernaw <[email protected]> Co-authored-by: nathanvaughan-NOAA <[email protected]> Co-authored-by: rklasky <[email protected]> Part of #170: refactor distributions_base Part of #388 Part of #573: add normal_lpdf Part of #581: add lognormal_lpdf Part of #585: add multinomial_lpmf Part of #586 Part of #630 Part of #644 Part of #645 Part of #646 Part of #662 Part of #671 Part of #695 Part of #702 Close #672 Close #690

@brief

* 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. R ---- doc(FIMSFrame): Adds documentation to accessors and increased consistency doc(ParameterVector): Adds time-varying example to the vignette that is turned off by default but users can experiment doc(fims-demo): Adds example of a model that is built but not fit doc: Shares argument documentation across functions feat(create_default_*()): Creates default values for FIMS parameters feat(update_parameters()): Updates default values for FIMS parameters feat(initialize_*()): Uses methods::new() to set up FIMS modules feat(FIMSFit): Created FIMSFit as an S4 Class with [create_FIMSFit()] so people can also create a FIMSFit object without having to use [fit_fims()] and so the object returned by [fit_fims()] looks the same no matter if you want the uncertainty calculated or not via `get_sd`. Objects are not added to things to obj, opt, and report and instead they are explicitly returned as a slot in the S4 FIMSFit class feat(estimates): In FIMSFit feat(verbose): Uses cli_inform cli_abort. Users can now set the global verbose level through `options(rlib_message_verbosity = "quiet")` to stop cli::cli_inform() messages from coming through. This allows for the verbose argument to be removed from all functions. And, [is_fims_verbose()] can check internally in functions to see if FIMS is currently verbose. fix(data1): Renamed from data_mile1 and adds length data fix(fims-demo): Updates vignette doi Bai et al. fix(FIMSFrame): Allows for subsetting of multiple fleets with %in% fix(plot.FIMSFrame): Adds y and ... for plot to be properly documented where previously we only had x, which led to scales not being seen as a package that was needed. The methods proposed in #672 was a work around where this commit fixes the problem. fix(Rcpp_Parameter*): Moves to zzz.R because when in operators it was leading to warnings when compiling in R. The movement allows this file to be ran before the others and it does not matter if Rcpp_Parameter or Rcpp_ParameterVector is exported/defined. I also worked on the formatting of those functions as well as combining the documentation rather for similar, i.e., methods. refactor(cli): Updates error message to use cli formatting refactor(DESCRIPTION): Adds packages * Adds purrr, tidyr, tibble, stats * Removes tidyverse * Depends on R 4.1.0 because of the use of the native pipe, which is available in R version 4.1.0. Status-quo dependency was R 4.0. refactor(tests): convert tests to testthat format in test-unit-rcpp-interface-variable-vector.R C++ ---- doc: Remove authors, email from file headers, some cleanup to cpp file header with consistent use of @file, @brief, @details, and @copyright for every file in inst/include and notes. doc(mainpage): Adds mainpage for doxygen as discussed by the documentation group led by @Bai-Li-NOAA in July (notes [here]( https://docs.google.com/document/d/1tPCSSanZ7SHaSE5SMkPoYrZh_lsswe7o5gtEyJmA0DU/edit?tab=t.0#heading=h.enmw68u5r5hm)). doc(Parameter): Fully documents Parameter and ParameterVector matching documentation at the function definition with what is shown in Rcpp methods::show() inside R. doc(pos): Uses pos in position for time-varying so it does not seem like things can only vary with time. feat: add variable_map infrastructure * adds variable map as an object in information.hpp * adds std::vector<uint32_t> key to density_components_base * adds unique ID to VariableVector class and get_id function * resizes key and pass to densities in rcpp_distributions feat: Uses .estimated_m and .is_random_effect_m in interface feat(get_force_scalar): method in fims::Vector to return the first index if the vector is size one. feat(get_parameter_names): Gets parameter names from C++ fix: Sets unique key for all tracked parameter/derived value in Rcpp objects fix(information): add data error checks in information fix(rcpp_interface): add get and set id functions to fleet interface fix(multinomial_lpmf.hpp): make lpdf_vec to return 0 if data is missing fix(Parameter): Removes estimated_m fix(Makevars): Removes c++17 flag In favor of USE_CXX17 = "yes" and removes -w flag where this fix is known to work on Windows. fix(clear): Removes everything because there was some information from random effects that was not being cleared leading to crashes. Many functions in the C++ code were also changed to CamelCase such as Clear(). Refactored function names to match style of other member functions. clear() procedure creates a new instance of the information singleton object. fix: Removes log_sigma_recruit from the Beverton--Holt stock--recruitment interface because it is now a part of the distribution associated with log_devs fix(logging): Uses macros * Removes old logging * pretty format for output * added format string for json * created a logging vignette * Adds information about DFIMS_DEBUG information * Adds throw on error fix: Collapses methods using S4 Group Generic Functions fix: Defines methods for Ops, Math, and Summary fix: Updates parameter min/max default values refactor(model.hpp): Loops over all density modules to sum up joint negative log-likelihoods refactor: Adds i=0 in for loops because R CMD check was complaining about significant warnings in compiling the c++ code because i was not initialized. refactor(information): Improves readability refactor: Uses C++ 17 refactor: Renames SIMULATE_F to FIMS_SIMULATE_F refactor: Renames REPORT_F to FIMS_REPORT_F GitHub ---- chore: change actions/checkout@v3 to v4 feat: Adds call-spell-check.yml from {ghactions4r} to spellcheck with WORDLIST fix: Adds .json to .gitignore fix: Adds .vscode to .gitignore fix: Removes parallel tests because they were not helpful fix: revert sim_num to 100 to simulate 100 sets of test data (see tests/testthat/fixtures/simulate-integration-test-data.R) TODO: ---- * Remove code for processR in tests * Find TODO statements in documentation and add the documentation * think about renaming some of the Rcpp functions * cli_* needs to be implemented throughout the package * fix(fims-demo): Does not use returned object from fit_fims for plots * no metadata object found to revise superClass error with sdreport class * Add a standalone test (CI-only) for checking the speed of parallel runs * fix parallel tests to avoid comparing run time with serial execution Co-authored-by: Andrea-Havron-NOAA <[email protected]> Co-authored-by: Bai-Li-NOAA <[email protected]> Co-authored-by: ChristineStawitz-NOAA <[email protected]> Co-authored-by: cmlegault <[email protected]> Co-authored-by: Cole-Monnahan-NOAA <[email protected]> Co-authored-by: JaneSullivan-NOAA <[email protected]> Co-authored-by: iantaylor-NOAA <[email protected]> Co-authored-by: k-doering-NOAA <[email protected]> Co-authored-by: kellijohnson-NOAA <[email protected]> Co-authored-by: KyleShertzer-NOAA <[email protected]> Co-authored-by: msupernaw <[email protected]> Co-authored-by: nathanvaughan-NOAA <[email protected]> Co-authored-by: rklasky <[email protected]> Part of #170: refactor distributions_base Part of #388 Part of #573: add normal_lpdf Part of #581: add lognormal_lpdf Part of #585: add multinomial_lpmf Part of #586 Part of #630 Part of #644 Part of #645 Part of #646 Part of #662 Part of #671 Part of #695 Part of #702 Close #672 Close #690

@brief

* 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. R ---- doc(FIMSFrame): Adds documentation to accessors and increased consistency doc(ParameterVector): Adds time-varying example to the vignette that is turned off by default but users can experiment doc(fims-demo): Adds example of a model that is built but not fit doc: Shares argument documentation across functions feat(create_default_*()): Creates default values for FIMS parameters feat(update_parameters()): Updates default values for FIMS parameters feat(initialize_*()): Uses methods::new() to set up FIMS modules feat(FIMSFit): Created FIMSFit as an S4 Class with [create_FIMSFit()] so people can also create a FIMSFit object without having to use [fit_fims()] and so the object returned by [fit_fims()] looks the same no matter if you want the uncertainty calculated or not via `get_sd`. Objects are not added to things to obj, opt, and report and instead they are explicitly returned as a slot in the S4 FIMSFit class feat(estimates): In FIMSFit feat(verbose): Uses cli_inform cli_abort. Users can now set the global verbose level through `options(rlib_message_verbosity = "quiet")` to stop cli::cli_inform() messages from coming through. This allows for the verbose argument to be removed from all functions. And, [is_fims_verbose()] can check internally in functions to see if FIMS is currently verbose. fix(data1): Renamed from data_mile1 and adds length data fix(fims-demo): Updates vignette doi Bai et al. fix(FIMSFrame): Allows for subsetting of multiple fleets with %in% fix(plot.FIMSFrame): Adds y and ... for plot to be properly documented where previously we only had x, which led to scales not being seen as a package that was needed. The methods proposed in #672 was a work around where this commit fixes the problem. fix(Rcpp_Parameter*): Moves to zzz.R because when in operators it was leading to warnings when compiling in R. The movement allows this file to be ran before the others and it does not matter if Rcpp_Parameter or Rcpp_ParameterVector is exported/defined. I also worked on the formatting of those functions as well as combining the documentation rather for similar, i.e., methods. refactor(cli): Updates error message to use cli formatting refactor(DESCRIPTION): Adds packages * Adds purrr, tidyr, tibble, stats * Removes tidyverse * Depends on R 4.1.0 because of the use of the native pipe, which is available in R version 4.1.0. Status-quo dependency was R 4.0. refactor(tests): convert tests to testthat format in test-unit-rcpp-interface-variable-vector.R C++ ---- doc: Remove authors, email from file headers, some cleanup to cpp file header with consistent use of @file, @brief, @details, and @copyright for every file in inst/include and notes. doc(mainpage): Adds mainpage for doxygen as discussed by the documentation group led by @Bai-Li-NOAA in July (notes [here]( https://docs.google.com/document/d/1tPCSSanZ7SHaSE5SMkPoYrZh_lsswe7o5gtEyJmA0DU/edit?tab=t.0#heading=h.enmw68u5r5hm)). doc(Parameter): Fully documents Parameter and ParameterVector matching documentation at the function definition with what is shown in Rcpp methods::show() inside R. doc(pos): Uses pos in position for time-varying so it does not seem like things can only vary with time. feat: add variable_map infrastructure * adds variable map as an object in information.hpp * adds std::vector<uint32_t> key to density_components_base * adds unique ID to VariableVector class and get_id function * resizes key and pass to densities in rcpp_distributions feat: Uses .estimated_m and .is_random_effect_m in interface feat(get_force_scalar): method in fims::Vector to return the first index if the vector is size one. feat(get_parameter_names): Gets parameter names from C++ fix: Sets unique key for all tracked parameter/derived value in Rcpp objects fix(information): add data error checks in information fix(rcpp_interface): add get and set id functions to fleet interface fix(multinomial_lpmf.hpp): make lpdf_vec to return 0 if data is missing fix(Parameter): Removes estimated_m fix(Makevars): Removes c++17 flag In favor of USE_CXX17 = "yes" and removes -w flag where this fix is known to work on Windows. fix(clear): Removes everything because there was some information from random effects that was not being cleared leading to crashes. Many functions in the C++ code were also changed to CamelCase such as Clear(). Refactored function names to match style of other member functions. clear() procedure creates a new instance of the information singleton object. fix: Removes log_sigma_recruit from the Beverton--Holt stock--recruitment interface because it is now a part of the distribution associated with log_devs fix(logging): Uses macros * Removes old logging * pretty format for output * added format string for json * created a logging vignette * Adds information about DFIMS_DEBUG information * Adds throw on error fix: Collapses methods using S4 Group Generic Functions fix: Defines methods for Ops, Math, and Summary fix: Updates parameter min/max default values refactor(model.hpp): Loops over all density modules to sum up joint negative log-likelihoods refactor: Adds i=0 in for loops because R CMD check was complaining about significant warnings in compiling the c++ code because i was not initialized. refactor(information): Improves readability refactor: Uses C++ 17 refactor: Renames SIMULATE_F to FIMS_SIMULATE_F refactor: Renames REPORT_F to FIMS_REPORT_F GitHub ---- chore: change actions/checkout@v3 to v4 feat: Adds call-spell-check.yml from {ghactions4r} to spellcheck with WORDLIST fix: Adds .json to .gitignore fix: Adds .vscode to .gitignore fix: Removes parallel tests because they were not helpful fix: revert sim_num to 100 to simulate 100 sets of test data (see tests/testthat/fixtures/simulate-integration-test-data.R) TODO: ---- * Remove code for processR in tests * Find TODO statements in documentation and add the documentation * think about renaming some of the Rcpp functions * cli_* needs to be implemented throughout the package * fix(fims-demo): Does not use returned object from fit_fims for plots * no metadata object found to revise superClass error with sdreport class * Add a standalone test (CI-only) for checking the speed of parallel runs * fix parallel tests to avoid comparing run time with serial execution Co-authored-by: Andrea-Havron-NOAA <[email protected]> Co-authored-by: Bai-Li-NOAA <[email protected]> Co-authored-by: ChristineStawitz-NOAA <[email protected]> Co-authored-by: cmlegault <[email protected]> Co-authored-by: Cole-Monnahan-NOAA <[email protected]> Co-authored-by: JaneSullivan-NOAA <[email protected]> Co-authored-by: iantaylor-NOAA <[email protected]> Co-authored-by: k-doering-NOAA <[email protected]> Co-authored-by: kellijohnson-NOAA <[email protected]> Co-authored-by: KyleShertzer-NOAA <[email protected]> Co-authored-by: msupernaw <[email protected]> Co-authored-by: nathanvaughan-NOAA <[email protected]> Co-authored-by: rklasky <[email protected]> Part of #170: refactor distributions_base Part of #388 Part of #573: add normal_lpdf Part of #581: add lognormal_lpdf Part of #585: add multinomial_lpmf Part of #586 Part of #630 Part of #644 Part of #645 Part of #646 Part of #662 Part of #671 Part of #695 Part of #702 Close #672 Close #690

@brief

* 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. R ---- doc(FIMSFrame): Adds documentation to accessors and increased consistency doc(ParameterVector): Adds time-varying example to the vignette that is turned off by default but users can experiment doc(fims-demo): Adds example of a model that is built but not fit doc: Shares argument documentation across functions feat(create_default_*()): Creates default values for FIMS parameters feat(update_parameters()): Updates default values for FIMS parameters feat(initialize_*()): Uses methods::new() to set up FIMS modules feat(FIMSFit): Created FIMSFit as an S4 Class with [create_FIMSFit()] so people can also create a FIMSFit object without having to use [fit_fims()] and so the object returned by [fit_fims()] looks the same no matter if you want the uncertainty calculated or not via `get_sd`. Objects are not added to things to obj, opt, and report and instead they are explicitly returned as a slot in the S4 FIMSFit class feat(estimates): In FIMSFit feat(verbose): Uses cli_inform cli_abort. Users can now set the global verbose level through `options(rlib_message_verbosity = "quiet")` to stop cli::cli_inform() messages from coming through. This allows for the verbose argument to be removed from all functions. And, [is_fims_verbose()] can check internally in functions to see if FIMS is currently verbose. fix(data1): Renamed from data_mile1 and adds length data fix(fims-demo): Updates vignette doi Bai et al. fix(FIMSFrame): Allows for subsetting of multiple fleets with %in% fix(plot.FIMSFrame): Adds y and ... for plot to be properly documented where previously we only had x, which led to scales not being seen as a package that was needed. The methods proposed in #672 was a work around where this commit fixes the problem. fix(Rcpp_Parameter*): Moves to zzz.R because when in operators it was leading to warnings when compiling in R. The movement allows this file to be ran before the others and it does not matter if Rcpp_Parameter or Rcpp_ParameterVector is exported/defined. I also worked on the formatting of those functions as well as combining the documentation rather for similar, i.e., methods. refactor(cli): Updates error message to use cli formatting refactor(DESCRIPTION): Adds packages * Adds purrr, tidyr, tibble, stats * Removes tidyverse * Depends on R 4.1.0 because of the use of the native pipe, which is available in R version 4.1.0. Status-quo dependency was R 4.0. refactor(tests): convert tests to testthat format in test-unit-rcpp-interface-variable-vector.R C++ ---- doc: Remove authors, email from file headers, some cleanup to cpp file header with consistent use of @file, @brief, @details, and @copyright for every file in inst/include and notes. doc(mainpage): Adds mainpage for doxygen as discussed by the documentation group led by @Bai-Li-NOAA in July (notes [here]( https://docs.google.com/document/d/1tPCSSanZ7SHaSE5SMkPoYrZh_lsswe7o5gtEyJmA0DU/edit?tab=t.0#heading=h.enmw68u5r5hm)). doc(Parameter): Fully documents Parameter and ParameterVector matching documentation at the function definition with what is shown in Rcpp methods::show() inside R. doc(pos): Uses pos in position for time-varying so it does not seem like things can only vary with time. feat: add variable_map infrastructure * adds variable map as an object in information.hpp * adds std::vector<uint32_t> key to density_components_base * adds unique ID to VariableVector class and get_id function * resizes key and pass to densities in rcpp_distributions feat: Uses .estimated_m and .is_random_effect_m in interface feat(get_force_scalar): method in fims::Vector to return the first index if the vector is size one. feat(get_parameter_names): Gets parameter names from C++ fix: Sets unique key for all tracked parameter/derived value in Rcpp objects fix(information): add data error checks in information fix(rcpp_interface): add get and set id functions to fleet interface fix(multinomial_lpmf.hpp): make lpdf_vec to return 0 if data is missing fix(Parameter): Removes estimated_m fix(Makevars): Removes c++17 flag In favor of USE_CXX17 = "yes" and removes -w flag where this fix is known to work on Windows. fix(clear): Removes everything because there was some information from random effects that was not being cleared leading to crashes. Many functions in the C++ code were also changed to CamelCase such as Clear(). Refactored function names to match style of other member functions. clear() procedure creates a new instance of the information singleton object. fix: Removes log_sigma_recruit from the Beverton--Holt stock--recruitment interface because it is now a part of the distribution associated with log_devs fix(logging): Uses macros * Removes old logging * pretty format for output * added format string for json * created a logging vignette * Adds information about DFIMS_DEBUG information * Adds throw on error fix: Collapses methods using S4 Group Generic Functions fix: Defines methods for Ops, Math, and Summary fix: Updates parameter min/max default values refactor(model.hpp): Loops over all density modules to sum up joint negative log-likelihoods refactor: Adds i=0 in for loops because R CMD check was complaining about significant warnings in compiling the c++ code because i was not initialized. refactor(information): Improves readability refactor: Uses C++ 17 refactor: Renames SIMULATE_F to FIMS_SIMULATE_F refactor: Renames REPORT_F to FIMS_REPORT_F GitHub ---- chore: change actions/checkout@v3 to v4 feat: Adds call-spell-check.yml from {ghactions4r} to spellcheck with WORDLIST fix: Adds .json to .gitignore fix: Adds .vscode to .gitignore fix: Removes parallel tests because they were not helpful fix: revert sim_num to 100 to simulate 100 sets of test data (see tests/testthat/fixtures/simulate-integration-test-data.R) TODO: ---- * Remove code for processR in tests * Find TODO statements in documentation and add the documentation * think about renaming some of the Rcpp functions * cli_* needs to be implemented throughout the package * fix(fims-demo): Does not use returned object from fit_fims for plots * no metadata object found to revise superClass error with sdreport class * Add a standalone test (CI-only) for checking the speed of parallel runs * fix parallel tests to avoid comparing run time with serial execution Co-authored-by: Andrea-Havron-NOAA <[email protected]> Co-authored-by: Bai-Li-NOAA <[email protected]> Co-authored-by: ChristineStawitz-NOAA <[email protected]> Co-authored-by: cmlegault <[email protected]> Co-authored-by: Cole-Monnahan-NOAA <[email protected]> Co-authored-by: JaneSullivan-NOAA <[email protected]> Co-authored-by: iantaylor-NOAA <[email protected]> Co-authored-by: k-doering-NOAA <[email protected]> Co-authored-by: kellijohnson-NOAA <[email protected]> Co-authored-by: KyleShertzer-NOAA <[email protected]> Co-authored-by: msupernaw <[email protected]> Co-authored-by: nathanvaughan-NOAA <[email protected]> Co-authored-by: rklasky <[email protected]> Part of #170: refactor distributions_base Part of #388 Part of #573: add normal_lpdf Part of #581: add lognormal_lpdf Part of #585: add multinomial_lpmf Part of #586 Part of #630 Part of #644 Part of #645 Part of #646 Part of #662 Part of #671 Part of #695 Part of #702 Close #672 Close #690

kellijohnson-NOAA added kind: refactor Restructure code to improve the implementation of FIMS P3 low priority task theme: code cleanup labels Aug 7, 2024

kellijohnson-NOAA added this to the Q2 milestone Aug 7, 2024

kellijohnson-NOAA mentioned this issue Oct 2, 2024

Add fimsfit #670

Merged

kellijohnson-NOAA mentioned this issue Oct 15, 2024

add data back to fleet #675

Merged

kellijohnson-NOAA mentioned this issue Nov 4, 2024

Update fims-demo.Rmd #680

Closed

Andrea-Havron-NOAA mentioned this issue Nov 4, 2024

[Refactor]: when should FIMS switch to TMBad? #210

Open

This was referenced Nov 25, 2024

Refactor distribution names #685

Merged

Add R wrapper functions to prepare parameters for running FIM #688

Merged

jbigman-NOAA assigned jbigman-NOAA and unassigned jbigman-NOAA Dec 2, 2024

iantaylor-NOAA added a commit that referenced this issue Dec 5, 2024

chore: add call-spell-check.yml from {ghactions4r} into the FIMS GHA …

c3f6ced

…workflows #662 Co-authored-by: Jane Sullivan <[email protected]> Co-authored-by: Kathryn Doering <[email protected]>

iantaylor-NOAA added a commit that referenced this issue Dec 5, 2024

chore: change actions/checkout@v3 to v4 #662

e5833a4

iantaylor-NOAA added a commit that referenced this issue Dec 5, 2024

chore: add call-spell-check.yml from {ghactions4r} into the FIMS GHA …

7078811

…workflows related to #662 Co-authored-by: Jane Sullivan <[email protected]> Co-authored-by: Kathryn Doering <[email protected]>

iantaylor-NOAA added a commit that referenced this issue Dec 5, 2024

chore: change actions/checkout@v3 to v4 #662

87fa60e

JaneSullivan-NOAA mentioned this issue Dec 5, 2024

Dev chores spellcheck and checkout versions #689

Merged

kellijohnson-NOAA pushed a commit that referenced this issue Dec 5, 2024

chore: change actions/checkout@v3 to v4 #662

997209b

kellijohnson-NOAA added a commit that referenced this issue Dec 5, 2024

chore: Adds data_mile1 to all calls

6dba16d

Part of #662

kellijohnson-NOAA pushed a commit that referenced this issue Dec 5, 2024

chore: change actions/checkout@v3 to v4 #662

4698edc

kellijohnson-NOAA added a commit that referenced this issue Dec 5, 2024

chore: Adds data_mile1 to all calls

10ba7ed

Part of #662

This was referenced Dec 6, 2024

[Bug:] CreateTMBModel() segfaults with new version of Rcpp (1.0.13) #686

Closed

chore: Remove authors, email from file headers, some cleanup to cpp file header #695

Merged

MOshima-PIFSC mentioned this issue Dec 11, 2024

Dev fimsframe clean up #699

Merged

kellijohnson-NOAA mentioned this issue Dec 18, 2024

demo vignette modification suggestions #705

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[Developer Issue]: M2 Quality control task list #662

[Developer Issue]: M2 Quality control task list #662

kellijohnson-NOAA commented Aug 7, 2024 •

edited

Loading

Tasks

k-doering-NOAA commented Aug 7, 2024

[Developer Issue]: M2 Quality control task list #662

[Developer Issue]: M2 Quality control task list #662

Comments

kellijohnson-NOAA commented Aug 7, 2024 • edited Loading

Description

Tasks

k-doering-NOAA commented Aug 7, 2024

kellijohnson-NOAA commented Aug 7, 2024 •

edited

Loading