EuropeanIFCBGroup/iRfcb: v.0.7.0

New features

• New function ifcb_annotate_samples() to create manual classification .mat files compatible with the ifcb-analysis MATLAB repository, using PNG images organized in class named subfolders and a class2use.mat file.
• New function ifcb_zip_images_by_class() to zip each PNG subfolder with optional random sampling. Useful for preparing class-specific image archives for submission.
• Added a new diatom_include argument to ifcb_extract_biovolumes() and ifcb_is_diatom() for manually forcing specific taxa to be treated as diatoms (overrides WoRMS classification).
• Added a new timestamp_param argument to ifcb_get_ferrybox_data() allowing the Ferrybox timestamp column to be specified dynamically instead of being hard coded.
• Added a new max_time_diff_min argument to ifcb_get_ferrybox_data() controlling the maximum allowed time difference in minutes when matching Ferrybox data to requested timestamps.
• Added a new biovolume_only argument to ifcb_read_features() to allow reading only biovolume related columns, improving performance for large feature tables.
• Added a new add_trailing_numbers argument to ifcb_extract_annotated_images() to control whether a zero-padded numeric suffix based on the manual class index is appended to class names in the output filenames.
• Added a new include_classes argument to ifcb_prepare_whoi_plankton() to allow explicit selection of classes to include during processing.

Minor improvements and fixes

• Runnable examples are now wrapped in \donttest{} instead of \dontrun{}.
• Timestamp matching in ifcb_get_ferrybox_data() is now more flexible and can fall back to the closest available Ferrybox observation within the specified time window when no exact or rounded match is found.
• ifcb_summarize_biovolumes() and ifcb_extract_biovolumes() are now more flexible and accept individual .mat files in addition to folders.
• Improved performance of ifcb_extract_biovolumes() and ifcb_summarize_biovolumes().
• All data frame outputs are now consistently returned as tibbles.
• Updated IFCB example in ifcb_get_ecotaxa_example().
• Moved vignettes that required internet access to package articles to improve CRAN check reliability.
• Improved error handling across functions, with clearer and more consistent messages.
• EEA coastline data are now obtained from EEA map services, replacing direct file server downloads that were unstable.
• Test data are sourced from GitHub when not available on Figshare.
• ifcb_create_manual_file() and ifcb_create_empty_manual_file() now correctly handles NaN values in the classlist.

Deprecations

• ifcb_create_empty_manual_file() has been renamed to ifcb_create_manual_file().
• ifcb_match_taxa_names() is now superseded by SHARK4R::match_worms_taxa().
• Deprecated arguments:
  • mat_folder in ifcb_summarize_biovolumes() and ifcb_extract_biovolumes() (replaced by mat_files).
  • expected_checksum in ifcb_download_test_data().

Full Changelog: https://github.com/EuropeanIFCBGroup/iRfcb/compare/0.6.0...0.7.0