EuropeanIFCBGroup/iRfcb: v.0.7.0
Abstract
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
Publication details
- Journal / source
- Zenodo (CERN European Organization for Nuclear Research)
- Publication date
- 8 January 2026