NEWS.md

In iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

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 0.4.3

Minor improvements and fixes

• ifcb_summarize_biovolumes() now handles custom class lists.
• Updated documentation and vignettes.
• Improved speed of tests and vignette rendering.
• Removed unnecessary suggested packages: fs and shinytest.

iRfcb 0.4.2

Minor changes

• Updated documentation to pass CRAN checks.

iRfcb 0.4.1

Minor improvements and fixes

• Removed imager (replaced by png) in ifcb_extract_pngs() and base64enc dependencies.
• Added gamma argument to ifcb_extract_pngs().
• Updated vignettes.

iRfcb 0.4.0

New features

• Reorganized vignettes into multiple tutorials.
• Added verbose argument to functions:
• ifcb_download_test_data()
• ifcb_extract_biovolumes()
• ifcb_is_diatom()
• ifcb_read_features()
• ifcb_summarize_biovolumes()
• Promoted WoRMS helper (iRfcb:::retrieve_worms_records()) to top-level function: ifcb_match_taxa_names().

iRfcb 0.3.15

Minor improvements and fixes

• Fixed issue in ifcb_get_ferrybox_data() where multiple close ferrybox timestamps caused duplicate rows. Now returns only the nearest match.

iRfcb 0.3.14

Minor improvements and fixes

• Updated SHARK example in ifcb_get_shark_example() and ifcb_get_shark_colnames() for testing and documentation.

iRfcb 0.3.13

New features

• Added ifcb_merge_manual() to merge manual .mat datasets.
• Added ifcb_adjust_classes() to adjust classes in manual data.
• Added ifcb_create_class2use() to generate a class2use file.

iRfcb 0.3.12

New features

• Added ifcb_create_empty_manual_file() to create new manual .mat files.
• Added ifcb_annotate_batch() to annotate multiple .mat files in a batch based on .png images.

Minor improvements and fixes

• Compressed .mat files to save space using do_compression argument in:
• ifcb_correct_annotation()
• ifcb_replace_mat_values()

iRfcb 0.3.11

New features

• Added ifcb_summarize_png_metadata() to summarize EcoTaxa metadata.
• Added ifcb_get_ecotaxa_example() to extract EcoTaxa headers and example data.

Minor improvements and fixes

• Large ZIP files can now be split using helper iRfcb:::split_large_zip() in ifcb_zip_pngs().

Deprecations

• Deprecated ifcb_summarize_png_data() (replaced by ifcb_summarize_png_counts()).

iRfcb 0.3.10

Minor improvements and fixes

• Updated documentation and examples.

Deprecations

• Removed deprecated function ifcb_get_svea_position().
• Removed helper iRfcb:::handle_missing_positions().
• Deprecated arguments manual_folder, feature_folder, and class_folder in several functions (ifcb_count_mat_annotations(), ifcb_extract_biovolumes(), ifcb_read_features(), ifcb_summarize_biovolumes().

iRfcb 0.3.9

Minor improvements and fixes

• Fixed edge case where nrow(taxa_list) == 0 in ifcb_count_mat_annotations().
• Added mat_recursive option to ifcb_count_mat_annotations().
• Added manual_recursive option to ifcb_extract_annotated_images() and ifcb_zip_matlab().
• Added roi_recursive option to ifcb_extract_annotated_images().
• Added data_recursive option to ifcb_zip_matlab().
• Added feature_recursive option to ifcb_zip_matlab().

iRfcb 0.3.8

Minor improvements and fixes

• Added marine_only to ifcb_is_diatom(), iRfcb:::retrieve_worms_records(), ifcb_summarize_biovolumes() and ifcb_extract_biovolumes().
• Added feature_recursive to ifcb_extract_biovolumes() and ifcb_summarize_biovolumes().
• Added mat_recursive to ifcb_extract_biovolumes() and ifcb_summarize_biovolumes().
• Added hdr_recursive to ifcb_summarize_biovolumes().
• Extracted helper function from ifcb_is_diatom().

iRfcb 0.3.7

New features

• Added classifier name to output from MATLAB extraction in ifcb_summarize_biovolumes().

iRfcb 0.3.6

Minor improvements and fixes

• Removed Öresund from included Baltic Sea shape file used in ifcb_is_in_basin().
• Updated SHARK column names for compatibility in ifcb_get_shark_example() and ifcb_get_shark_colnames().

iRfcb 0.3.5

Minor improvements and fixes

• Improved error handling in WoRMS API calls with multiple attempts in iRfcb:::retrieve_worms_records().
• Updated package title.

Deprecations

• Deprecated ifcb_get_svea_position() (replaced by ifcb_get_ferrybox_data()).

iRfcb 0.3.4

Minor improvements and fixes

• Added option to summarize biovolumes from manual files in ifcb_summarize_biovolumes().
• Added sleep_time parameter for ifcb_download_test_data().

iRfcb 0.3.3

Minor improvements and fixes

• Fixed manual .mat count edge case.
• Switched to curl for downloads.
• Parameterized PSD micron factor in ifcb_psd() with argument micron_factor.
• General clean-up of minor improvements and fixes.

iRfcb 0.3.2

Minor improvements and fixes

• Replaced test data with a smaller dataset.
• Improved unit test coverage.

iRfcb 0.3.1

Minor improvements and fixes

• Corrected documentation errors.

iRfcb 0.3.0

New features

• Introduced unit testing with testthat for improve stability.
• Improved consistency and functionality across multiple functions.

iRfcb 0.2.6

Minor improvements and fixes

• Minor update of documentation for clarity and consistency.

iRfcb 0.2.5

Minor improvements and fixes

• Improved pkgdown webpage.
• Refined tutorial content.
• General code cleanup and internal documentation improvements.

iRfcb 0.2.4

Minor improvements and fixes

• Moved example documentation to vignettes.
• Added verbose argument to several functions to provide detailed progress messages during execution.

iRfcb 0.2.3

Minor improvements and fixes

• ifcb_replace_mat_values() now only handles .mat files in the manual_folder.
• Made more examples runnable by including relevant example data in the package.

iRfcb 0.2.2

Minor improvements and fixes

• ifcb_is_near_land() now returns NA if coordinates passed to the function contain NA values.

iRfcb 0.2.1

New features

• Added ifcb_get_trophic_type() to assign trophic strategy to taxa.

Minor improvements and fixes

• ifcb_get_shark_colnames():
• Added SHARK columns: WADEP, PDMET, METFP, IFCBNO, TRPHY, ABUND, and BIOVOL.
• Removed deprecated columns: SAMPLE_TIME, ABUND_UNITS_PER_LITER, BIOVOL_PER_SAMPLE, BIOVOL_PER_LITER, C_CONC_PER_LITER, and SEA_BASIN.

iRfcb 0.2.0

New features

• New functions:
• extract_aphia_id(): Extract AphiaID from WoRMS record.
• extract_class(): Extract taxonomic class from WoRMS record.
• handle_missing_positions(): Handle missing positions by rounding timestamps.
• ifcb_extract_biovolumes(): Compute biovolumes and carbon from IFCB data.
• ifcb_get_shark_colnames(): Retrieve column names for SHARK submission.
• ifcb_get_svea_position(): Extract GPS coordinates from ferrybox data.
• ifcb_is_diatom(): Identify diatoms in a taxa list.
• ifcb_is_in_basin(): Check whether points fall inside a sea basin.
• ifcb_psd_plot(): Create particle size distribution plots from IFCB data.
• ifcb_read_features(): Read IFCB feature files from a specified folder.
• ifcb_summarize_biovolumes(): Summarize biovolumes and carbon content.
• ifcb_summarize_class_counts(): Count TreeBagger classifier outputs.
• ifcb_which_basin(): Return name of sea basin a point belongs to.
• summarize_TBclass(): Summarize TreeBagger classifier results.
• vol2C_lgdiatom(): Convert biovolume to carbon for large diatoms.
• vol2C_nondiatom(): Convert biovolume to carbon for non-diatom protists.

Minor improvements and fixes

• Fixed issue in ifcb_read_hdr_data() where gps_only filtering could fail.
• Extended tutorial to include examples using newly added functions.

iRfcb 0.1.2

Minor improvements and fixes

• Fixed edge case in ifcb_volume_analyzed() when inhibition time == 0 (#2).

iRfcb 0.1.1

Minor improvements and fixes

• Fixed warning in ifcb_is_near_land() by applying sf::st_wrap_dateline() only when the CRS is geographic.
• Updated function documentation for consistency.

iRfcb 0.1.0

Initial development release of iRfcb.

Features

• Core functionality for reading and analyzing IFCB data, including:
• ifcb_convert_filenames()
• ifcb_correct_annotation()
• ifcb_count_mat_annotations()
• ifcb_create_manifest()
• ifcb_download_test_data()
• ifcb_extract_annotated_images()
• ifcb_extract_classified_images()
• ifcb_extract_pngs()
• ifcb_get_mat_names()
• ifcb_get_mat_variables()
• ifcb_get_runtime()
• ifcb_is_near_land()
• ifcb_psd()
• ifcb_py_install()
• ifcb_read_hdr_data()
• ifcb_read_summary()
• ifcb_replace_mat_values()
• ifcb_run_image_gallery()
• ifcb_summarize_png_data()
• ifcb_volume_analyzed_from_adc()
• ifcb_volume_analyzed()
• ifcb_zip_matlab()
• ifcb_zip_pngs()

iRfcb documentation built on April 16, 2025, 1:09 a.m.