Changelog

Source: NEWS.md

atlantio 0.2.0

• generate_calibration_table() supports is_factor, when true, min and maxare interpreted relative to the current value of the parameter rather than as absolute bounds.
• atlantis_load_files() no longer drops files when several files of the same type are passed, and skips files of unsupported type (e.g. unknown, xml_file) with a warning instead of erroring.
• read_txt_files() classifies DietCheck outputs as diet and DetailedDietCheck outputs as diet_detailed, and always returns a type.
• create_time_series_biomass() now detects all cohorts of groups with 10 or more age classes (the cohort index was truncated to its last digit).
• generate_calibration_table() no longer errors on per_box parameters.
• require_valid_group() reports only the groups that are missing or turned off, instead of all groups passed.
• Move sf to Suggests.
• Add calibrar script.

atlantio 0.1.0

• Initial version. The input/output functionalities of the calypso package have been extracted into this package; the Shiny application now lives in calypso, which builds on top of atlantio.
• Includes:
  • list_atlantis_parameters() that returns the list of Atlantis parameters for a supported Atlantis version (see the new dataset atlantis_supported_versions);
  • the S7 class Atlantis that represents an Atlantis model, with the constructor new_atlantis() and the loader atlantis_load_files();
  • reading functions for Atlantis files: read_atlantis_files(), read_bgm(), read_nc(), read_prm(), read_prm_files(), read_group_file(), read_txt_files(), read_xml();
  • a prm writer: write_prm();
  • parameter file generation with generate_file() (run file only);
  • S7 methods for Atlantis objects: print(), create_diet_table(), create_foodweb(), create_time_series(), create_time_series_biomass(), generate_calibration_table().