ageproR version 0.9.0

• Default current version AGEPRO input file format is set to AGEPRO VERSION 4.25.
  • Added agepro40_inpfile_string for AGEPRO VERSION 4.0 compatibility.
  • Improved AGEPRO Input File Format Version validation command line messages
    • Warning message is more clarified if AGEPRO VERSION 4.0 was detected.
    • Assert for valid strings and supported input file formats
• Auxiliary Output Flag (auxfile_output_flag)
  • All remaining instances of output_stock_summary were renamed to auxfile_output_flag.
    • Renamed JSON field summary_output_flag -> auxiliary_output_flag
    • options_output: param summary_report -> auxiliary_flag
  • Additional Auxiliary Output Flag parameter added to match specifications introduced in AGEPRO-GUI 4.3.6 and the December 2025 version of the AGEPRO Reference Manual (#98)
  • Supported Input File format validation is based on "Current Version" and AGEPRO VERSION 4.0 Input File Format (enable_agepro40_format):
    • If enable_agepro40_format is TRUE, check if value is logical or (0,1); if FALSE, check if value matches one of the Valid Auxiliary Output Flags (valid_aux_output_flags = c(0,1,2,3,4)).
• Updated testthat example to use AGEPRO Calculation Model's 4.25 updated Example 1 Input Model:
  • Added AGEPRO Example 1 (AGEPRO VERSION 4.25 input format);
    • Exported Example 1 Model data to new example JSON file Example1.json
  • test-agepro_model.R: Added checks to see if Example1 Input File and Bootstrap File Exists. Removed set_bootstrap_file test
  • Previous example test example file ageproInput.INP is replaced by AGEPRO_GUI Example 4 (AGEPRO VERSION 4.0)
    • Added Example 4 Bootstrap File; Example4_UKU.INP: Modified bootstrap_file to be a relative path.
• bootstrap_file relative filepaths can be verified:
  • Check the path of dirname of the input file, being read via file connection, plus the bootstrap_file relative filepath exists.
    If found save relative filepath to bootstrap_file. Otherwise, use working directory and use original bootstrap path validation.
  • This has a side effect of printing out absolute paths which affects testthat snapshots, that varies the output of the bootstrap_file causing test snapshot errors.
    • Fixup test-agepro_model.R : Substitute bootstrap_file output value path w/ fixed value <path>
• Refactor out validate_logical_parameter function from validation.R to as a options_output private helper method
• JSON inupt file
  • ver_json_format is now 2 (Changes to the JSON input format will increment up +1)
    • Fix inconsistencies (ver_jsonfile_format -> ver_json_format) causing NULL values
  • JSON fields renamed to be more consistent with the AGEPRO Reference Manual Table 3
    • summary_output_flag -> auxiliary_output_flag
    • process_error_aux_data_flag -> process_dataflag
    • report_precentile_value -> perc_report_value
    • biomass_scale -> scale_biomass
    • recruitment_scale -> scale_recruitment
    • stock_size_scale -> scale_stock_size
• Rename
  • assert_inpfile_version -> check_inpfile_version
  • parameter process_error_aux_files -> process_error_datafiles
  • function output_data_frame -> export_df
  • param export_r_data_frame -> export_df
• Bugfixes to read_inp_file trycatch error handling.
  • cli tweaks to show "error conditions"
  • Suppress enable_percentile_summary setup messages when resetting projection analysis types.
  • Fixed an erroneous call resetting enable_percentage_summary value.
• Updated README: Fixes and updated links from nmfs-ost migration (#96, #95)
• Update roxygen to 7.3.3

ageproR version 0.8.0

• Recruitment
  • Added empirical_ssb for Empirical Recruit Per Spawning Mass Distribution (Recruitment model 2) (#76)
  • Added parametric_autocorrelated_error as a base R6Class for Parametric Recruitment w/ Autocorrelated Lognormal Errors (#75)
    • Added berverton_holt_autocorrelated_error for Beverton-Holt w/ Autocorrelated Lognormal Error (Model 10)
    • Added shepherd_curve_autocorrelated_error for Shepherd Curve w/ Autocorrelated Lognormal Error (Model 11)
    • Added ricker_curve_autocorrelated_error for Ricker Curve w/ Autocorrelated Lognormal Error (Model 12)
  • Recruitment models 2, 10, 11, 12 added to list to valid recruitment numbers, and can be passed through set_recruit_model function.
  • Allow active binding recruitment fields (recruit_scaling_factor, ssb_scaling_factor, and max_recruit_obs) to be settable.
  • Empirical observation tables
    • Added obs_table parameter to set observation data at initialization. Default is NULL, generating default values, the original behavior.
    • Added method to set empirical recruitment observation data from data frames
  • Recruitment cli tweaks
    • cli tweaks improve readability with Recruitment Model and Name on Rconsole.
      • print now shows max_recruit_obs (#71)
    • Rename print_input_option_name -> print_process_error_fields
    • Minor read_inp_lines message tweak to clarify recruitment time period range.
  • Consolidated validate_numeric_substrings code into read_inp_numeric_lines function
  • Added option to toggle verbosity when setting new recruitment models via set_recruit_model
• Options
  • Consistency cli tweaks between Option classes
  • Renamed options-related files with option prefix and simplified some R6Classes names:
    • renamed R script max_bounds.R -> options_max_bounds.R
    • renamed R script user_percentile_summary.R -> options_percentile_summary.R
      • renamed R6Class user_percentile_summary -> percentile_summary
    • renamed R script reference_points.R -> options_reference_points.R
    • renamed R script scaling_factors.R -> options_scaling_factors.R
    • renamed R script retrospective_adjustments.R -> options_retrospective_adjustments.R
    • renamed R script output_options.R -> options_output.R
      • renamed R6class output_options -> options_output
    • renamed R script optional_options_flags.R -> option_flags.R
      • renamed R6Class optional_optional_flags -> option_flags
  • "options w/ options_flags" (option_flag class reference for: max_bounds, percentile_summary, reference_points, scaling_factors, retrospective_adjustments)
    • Fixed an issue where option_flags reference class was improperly referenced, causing unintended consequences using multiple agepro_model instances (#85)
      • Make option_flag R6class a non-shared Reference, and instantiate reference per agepro_model class instance.
      • During agepro_model instantiation, each "options w/ options_flags" is instantiated with an option_flag class reference.
    • Use formals to detect parameter defaults to determine option_flag is enabled at initialization:
      • max_bounds, percentile_summary, reference_points, scaling_factors: Initialize with a non-default parameter: set its flag to TRUE; If all class parameters match default values, set the flag to FALSE.
      • retrospective_adjustments: removed default value for retro_adjust. If retrospective_adjust is missing in a new instances of this class, set enable_retrospective_adjustments to FALSE. Otherwise, its TRUE
  • Fixup option_flags inconsistencies, messages
• cli consistency tweaks (R message format)
  • Reworded Rconsole to represent the keyword parameter class field names.
    • Console alert symbols ℹ️ (or i) focuses on keyword parameter classes fields; ◀️ (or <) for a interface event (or input line read)
  • Output from initializing agepro_model classes or "printing" AGEPRO keyword parameters classes, will print under the R message format.
    • This resolves an issue with console output changes with RStudio 2025.05.0+496.
    • Pass print_parameter_table output through capture_output_as_message
      • Replaces use of tibbles for output; Removes tibble dependency.
      • Replaces redundant function cli_print_process_error_table in process_error class.
  • Added verbosity toggle to specifically show General Parameters to R console during agepro_model initialization. TRUE by default.
• Bootstrap
  • Clarified bootstrap_file warning message for relative path cases
  • cli fix to show Bootstrap File at agepro_model initialization
• Replace test AGEPRO input File, Bootstrap File, and json input file with AGEPRO-GUI Hawaii Uku Example, based on 2020 Hawaii Uku (Aprion virescens) Assessment.
  • Hawaii Uku JSON input file imported from Hawaii Uku AGEPRO input file.
  • Added description file of example.
• Added Vignette as "Article" format (#84)
  • Includes AGEPRO Input File Keyword Parameter Structure and stub for JSON experimental file
• README update (#88)

ageproR version 0.7.3

• agepro_inp_model can be initialized with general agepro model parameters. This change will be consistent with agepro_model and agepro_json_model. (#64)
  • The default method to generate agepro_inp_model remains the same.
  • Fixup/Improve WARNING messages for NULL Recruitment Model Data and Invalid Bootstrap File
• Added testthat for basic unit testing scripts (#48)
  • added withr dependency to help with testthat scripts
• Added model_name parameter when initializing case_id. New agepro_model will include "Unnamed AGEPRO model" as model_name.
• Updated README
• removed redundant general_params parameter checks during agepro_model initialization

ageproR version 0.7.2

• Use version string (line 1) from AGEPRO Input File to correctly check input file version format against the "current version" input file string (currentver_inpfile_string)
• Validation checks for Invalid recruitment model data from NULL or Deprecated Recruitment model 9, when importing and exporting to AGEPRO Input File and JSON Input file (#54)
  • Interrupts export to AGEPRO Input File, if invalid recruitment model data found.
  • JSON input file: Nullify recruitData, if invalid recruitment model data found.
• rename set_projection_analyses -> setup_projection_analyses_value
  • Function now checks input 'type' parameter value before assigning to projection_analyses_type
• Error message clarifications

ageproR version 0.7.1

Note

This bugfix version reverts AGEPRO Input File format back to the AGEPRO VERSION 4.0.

• Reverted to AGEPRO VERSION 4.0 as currentver_inpfile_string. Input files will be written to AGEPRO VERSION 4.0
  • Supported_inpfile_versions are: currentver_inpfile_string, AGEPRO VERSION 4.0 , AGEPRO VERSION 4.25
  • write_inp(overwrite_as_currentver = FALSE) save to AGEPRO Input File and keep the supported version of input file (AGEPRO VERSION 4.25)
• write_inp: Use withCallingHandlers to properly handle errors when retrieving AGEPRO Input File formatted Strings from keyword parameter classes (get_inp_lines)
• Rename agepro_inp_model private helper function set_inpfile_version -> write_inpfile_version
  • Includes warning if (Supported) AGEPRO Input File Version is not the "current version"
• Updated Roxygen

ageproR version 0.7.0

Warning

Note: AGEPRO input files will be saved as AGEPRO VERSION 4.25, in reflection to the future 4.25 update to AGEPRO.

• Added AGEPRO optput_options (OPTIONS)
  • Added optional options keyword parameters:
    • user_percentile_summary (PERC)
    • max_bounds (BOUNDS)
    • reference_points (REFPOINTS)
    • scaling_factors (SCALE)
    • retrospective_adjustments (RETROADJUST)
  • Data can be imported/exported to AGEPRO Input File and/or Experimental JSON Input File. (#12, #9)
  • optional_options_flag: a shared Reference class for optional options.
    • Contains logical flags to allow user to edit optional options fields: enable_user_percentile_summary, enable_reference points, enable_scaling_factors, enable_max_bounds, enable_retrospective adjustments.
      • (Re)set to NULL when output options classes is initialized. By default, using initialized default values, set flag to FALSE. Otherwise, set to TRUE. If read from AGEPRO Input File, set to TRUE.
      • Due to its shared references nature, explicitly collate optional_options_flags.R to load before the optional options class R files in DESCRIPTION.
  • Current AGEPRO Input File version is now AGEPRO VERSION 4.25 (currentver_inpfile_string): Reflecting changes in OPTIONS StockSummaryFlag to the new release the AGEPRO calculation engine.
    • AGEPRO input files now written to file under AGERPRO VERSION 4.25; Input data imported from AGEPRO VERSION 4.0 input files will be saved to current version format.
    • Remove supported AGEPRO Input file version AGEPRO VERSION 4.2
• Changed version json list format Experimental JSON Input File:
  • Renamed version.leagcyVer -> version.inpfile_string: Reflects AGEPRO input file version string
  • Replace version.ver with version.jsonfile_format: Numeric for JSON Input File format. Marked JSON format to 0 until AGEPRO Keyword Parameters is implemented on JSON Input File.
• Added diagnostic value ver_rpackage to return the ageproR version the agepro model was created.
• Toy Example AGEPRO Input File
  • Changed version of Toy Example AGEPRO Input File to AGEPRO VERSION 4.0
  • Added PERC and OUTPUT data to toy Example Agepro Input File
• Added validation function validate_logical_parameter to validate, handle, and convert potential logical values as numerical values to output_options active binding fields.
• Fixes:
  • Fixup/Clarify AGEPRO Input file import error messages
  • Fix/updated rstudioapi checking character version strings to see if VSCode is currently used when opening save file dialog. Refactor redundant check functions.
  • Added cli prompts when import_agepro_inp_model is used
  • Added alternative package install method pak::pkg_install example to README.

Full Changelog: v0.6.2...v0.7.0

ageproR version 0.6.2

• Order R6 methods as: public, active, private by @efletcherPIFSC in #51

Full Changelog: v0.6.1...v0.6.2

ageproR version 0.6.1

• Rename inplines -> inp_lines for consistency (#37)
• Rename general, bootstrap, process_error, and recruitment json_list active binding functions to json_list_object
• process_error (#47)
  • Cleanup proj_years validation code
  • Moved setup_projection_tables as a private helper method.
• Resolved tibble::as_tibble column name deprecation (#44)
• Updated Roxygen Dependency to 7.3.1

ageproR ver 0.6.0

• Added mortality_fraction_prior_spawn
  • Data can be imported/exported to AGEPRO Input File/Experimental JSON Input File
  • added BIOLOGICAL data to toy Example Agepro Input File
  • changing time_varying creates a new proportion_total_mortality_matrix with default values and the number of columns depends on the time_varying state. The behavior is similar to AGEPRO-GUI.
  • Explicitly state natural_mortality and fishing_mortailty to proportion_total_mortality_matrix to avoid ambiguity with gender abbreviations
• Improved projection_years validation: multiple assertions (from the checkmate package) can be prompted to Rconsole.
  • Wrapped sequence validation error check as a custom checkmate assertion.
• Fixed multi recruitment model number support for agepro_model set_recruit_model (#49)
  • Included multiple assertions (from checkmate) to check set_recruit_model argument is a numeric vector that matches a list of valid AGEPRO recruitment model numbers.
  • Added custom checkmate assertion wrapper to check set_recruit_model argument is empty or has multiple arguments.
• Update DESCRIPTION

ageproR version 0.5.1

• recruitment
  • Fixed an issue (#39) where a difference of number of recruitment models using the agepro_model function set_recruit_model only changed the Recruit Data collection object structure but did not change recruitment probability nor the num_rec_models general_param field.
    • Assert that the count of recruitment model number(s) (model_num) parameter matches num_recruit_models parameter at initialization and when importing recruitment data (read_inp_lines) from AGEPRO input files.
      • Added num_recruit_models parameter to recruitment initialization
      • Added Sequence years (seq_years) parameter to read_inp_files to update number of recruit models
    • agepro_model$set_recruit_model : This now initializes a new instance of the recruitment class, using the general_params field number of recruitment models (num_rec_models) value.
    • Use purrr::map to validate input for valid recruitment probabilities within the time projection year horizon for each recruitment model in Recruitment Probability (recruit_probability) active binding setter. Recruitment probabilities can be set after Recruitment
    • Use purrr::map to get (and validate) recruitment model numbers from Recruitment Model Data (recruit_data) input and update the Recruitment Model Number Vector in the recruit_data active binding setter.
  • Setter access to general recruitment active binding fields: recruit_scaling_factor, ssb_scaling_factor, max_recruit_obs, recruit_model_num_list, is set to private. These values can be set using methods of the recruitment class, such as during initialization.
  • Improved Recruitment Model Number Validation using the agepro_model function set_recruit_model
  • Code cleanup for consistency and clarity
    • Modularize setups for Recruitment probability(recruit_probability), Recruitment Model Number vector (recruit_model_num_list), and the Recruitment Model Data (recruit_data) into private helper functions.
    • Renamed field model_collection_list -> recruit_data for clarity.
    • Renamed common recruit_model active binding recruit_data -> json_recruit_data
    • Replaced observed_years to sequence_projection_years field.
    • Renamed recruitment's set_recruit_model function to initialize_recruit_model to reflect its intended functionality and set it as a private helper function.
    • Renamed field max_rec_obs -> max_recruit_obs
    • Renamed recruitment function inplines_recruit (and inplines_general from general_params) to get_inp_lines (#37)
    • Renamed recruitment parameter cat_verbose -> enable_cat_print
• Setter access to general_params active binding fields: yr_begin, yr_end, age_begin, age_end, num_pop_sims, num_fleets, num_rec_models, discards_present, seed is set to private. These values can be set using methods of the general_params class, such as during initialization. This behavior matches AGEPRO-GUI
• Simplified projection years validation checks to check for numeric
• Updated roxygen dependency to version 7.3.0
  • Replaced deprecated doctype package in with _PACKAGE_ roxygen package documentation (ageproR.R -> ageproR-package.R)