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