Codestin Search App

Andrea-Havron-NOAA · 2024-06-13T22:33:37Z

What is the feature?

Addresses issues [Developer Issue]: Add documentation to new files from refactor-distributions #612

How have you implemented the solution?

Added documentation of class members and functions. Also added documentation on the top of each file that explained the acronyms LPDF and LPMF.

Does the PR impact any other area of the project?

How to test this change

doxygen gha will pass

Developer pre-PR checklist

I relied on GitHub actions to 🧪 things for me while I sat on the 🛋️.

github-actions · 2024-06-13T22:33:52Z

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KyleShertzer-NOAA · 2024-06-14T16:53:39Z

The new documentation is an improvement. Looks good to me.

* issue #630 * update documentation style

@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

@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 NOAA-FIMS#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 NOAA-FIMS#170: refactor distributions_base Part of NOAA-FIMS#388 Part of NOAA-FIMS#573: add normal_lpdf Part of NOAA-FIMS#581: add lognormal_lpdf Part of NOAA-FIMS#585: add multinomial_lpmf Part of NOAA-FIMS#586 Part of NOAA-FIMS#630 Part of NOAA-FIMS#644 Part of NOAA-FIMS#645 Part of NOAA-FIMS#646 Part of NOAA-FIMS#662 Part of NOAA-FIMS#671 Part of NOAA-FIMS#695 Part of NOAA-FIMS#702 Close NOAA-FIMS#672 Close NOAA-FIMS#690

document density functions

9dbc36d

Andrea-Havron-NOAA requested review from Cole-Monnahan-NOAA, KyleShertzer-NOAA and cmlegault June 13, 2024 22:34

cmlegault reviewed Jun 14, 2024

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Comment thread inst/include/distributions/functors/multinomial_lpmf.hpp Outdated

cmlegault reviewed Jun 14, 2024

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Comment thread inst/include/distributions/functors/lognormal_lpdf.hpp

Andrea-Havron-NOAA added 2 commits June 14, 2024 06:53

update documentation style

7c95b27

fix documentation

fb47b01

Andrea-Havron-NOAA merged commit c30e54f into dev Jun 14, 2024

Andrea-Havron-NOAA deleted the 612-document-densities branch June 14, 2024 22:20

Andrea-Havron-NOAA mentioned this pull request Jun 14, 2024

[Developer Issue]: Add documentation to new files from refactor-distributions #612

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Andrea-Havron-NOAA added a commit that referenced this pull request Jun 18, 2024

document densities functions

5f73d9b

* issue #630 * update documentation style

Andrea-Havron-NOAA added a commit that referenced this pull request Jul 25, 2024

document densities functions

7af5dc7

* issue #630 * update documentation style

Andrea-Havron-NOAA added a commit that referenced this pull request Aug 27, 2024

document densities functions

f6cdcab

* issue #630 * update documentation style

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document densities from sprint 1 nll refactor#630

document densities from sprint 1 nll refactor#630
Andrea-Havron-NOAA merged 3 commits into
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Andrea-Havron-NOAA commented Jun 13, 2024

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