Version 0.5

iRfcb 0.5.0

New features

• Added NEWS.md to track package changes.
• New functions:
  • ifcb_download_dashboard_data() for fetching data from the WHOI IFCB Dashboard.
  • ifcb_download_whoi_plankton() for downloading WHOI-Plankton PNG datasets.
  • ifcb_prepare_whoi_plankton() to process WHOI data for integration.
• New vignette: vignette("whoi-plankton-data-integration").
• Python virtual environments can now be automatically activated by setting the USE_IRFCB_PYTHON environment variable when loading the package.
• Added scale bar support (#42) to:
  • ifcb_extract_pngs()
  • ifcb_extract_classified_images()
  • ifcb_extract_annotated_images()
• Added gamma argument to ifcb_extract_annotated_images () and ifcb_extract_classified_images() for gamma correction.
• ifcb_is_near_land():
  • Now returns a plot if plot = TRUE.
  • Added option to download EEA coastline data using the new argument source.
  • Deprecated the argument utm_zone, which is now determined automatically from longitude.

Minor improvements and fixes

• ifcb_read_hdr_data() now correctly handles files from IFCB Acquire 1.x.x.x (#41).
• ifcb_convert_filenames() is more efficient and now correctly parses filenames like "IFCB1_2010_309_192918" (#40).
• The default location of the venv path in ifcb_py_install() has changed to “~/.virtualenvs/iRfcb”.
• Added support for old .adc file format (IFCB1-6) by argument old_adc in:
  • ifcb_extract_pngs()
  • ifcb_extract_classified_images()
  • ifcb_extract_annotated_images()
• ifcb_read_mat() now returns consistent data structures aligned with R.matlab::readMat() (#50).

Deprecations

• ifcb_summarize_png_data() is now defunct (previously deprecated in version 0.3.11).
• Deprecated arguments:
  • adc_folder in ifcb_annotate_batch() (replaced by adc_files).
  • unclassified_id in ifcb_create_empty_manual_file() (replaced by classlist).
  • utm_zone in ifcb_is_near_land() (now determined automatically from longitude).
• ifcb_create_empty_manual_file() now accepts a complete class list via classlist, replacing the older unclassified_id.

iRfcb 0.5.1

Minor improvements and fixes

• Skipping certain internet-required tests on CRAN servers.
• Corrected help pages for ifcb_download_dashboard_data() and ifcb_download_whoi_plankton().

iRfcb 0.5.2

Minor improvements and fixes

• ifcb_download_test_data() gains checksum validation, keep_zip option, and improved retry logic.
• ifcb_extract_biovolumes() and ifcb_summarize_biovolumes() gain a drop_zero_volume option to exclude artifacts with zero biovolume
• ifcb_read_features() and ifcb_extract_biovolumes() now handles single feature_files correctly.
• Tests are now skipped if required resources are unavailable, improving stability in environments with limited access to external dependencies.