ifcb_download_dashboard_metadata() andifcb_list_dashboard_bins().diatom_include parameter toifcb_extract_biovolumes() andifcb_summarize_biovolumes() for manually forcing specifictaxa to be treated as diatoms (overrides WoRMS classification)(#65).bins parameter toifcb_psd() forselecting which bins to process.fea_v parameter toifcb_psd() forselecting feature-file version.use_plot_subfolders parameter toifcb_psd() to optionally save plots in subdirectories ofplot_folder based on flag status.flags parameter toifcb_psd_plot()to optionally add the quality flag annotation to the plot.ifcb_extract_biovolumes() now support both filenameformats_fea_v*.csv and_features_v*.csv,increasing compatibility with legacy and new output formats (#61).ifcb_read_features(),ifcb_summarize_png_metadata(),ifcb_summarize_biovolumes(), andifcb_extract_biovolumes() now include an optional parameterto select specific feature file versions (e.g.,_v2,_v4), allowing finer control over which feature data areread and processed.$data,$fits and$flagsdata frames returned byifcb_psd() now use full bin names(<sample>_<ifcb>) as sample names, improvinguniqueness and consistency with downstream workflows.$data and$fits data frames returnedbyifcb_psd() now preserves the original column names,including names starting with numbers or containing specialcharacters.ifcb_psd() hasbeen replaced by u in$data headers.$flags headers inifcb_psd() tousesample instead offile, ensuringconsistent naming across all outputs.ifcb_psd() whenplot_folder is specified,improving processing speed.ifcb_download_test_data() gains checksum validation,keep_zip option, and improved retry logic.ifcb_extract_biovolumes() andifcb_summarize_biovolumes() gain adrop_zero_volume option to exclude artifacts with zerobiovolumeifcb_read_features() andifcb_extract_biovolumes() now handles singlefeature_files correctly.ifcb_download_dashboard_data()andifcb_download_whoi_plankton().NEWS.md to track package changes.ifcb_download_dashboard_data() for fetching data fromthe WHOI IFCB Dashboard.ifcb_download_whoi_plankton() for downloadingWHOI-Plankton PNG datasets.ifcb_prepare_whoi_plankton() to process WHOI data forintegration.vignette("whoi-plankton-data-integration").USE_IRFCB_PYTHON environment variable whenloading the package.ifcb_extract_pngs()ifcb_extract_classified_images()ifcb_extract_annotated_images()gamma argument toifcb_extract_annotated_images () andifcb_extract_classified_images() for gamma correction.ifcb_is_near_land():plot = TRUE.source.utm_zone, which is nowdetermined automatically from longitude.ifcb_read_hdr_data() now correctly handles files fromIFCB Acquire 1.x.x.x (#41).ifcb_convert_filenames() is more efficient and nowcorrectly parses filenames like"IFCB1_2010_309_192918"(#40).ifcb_py_install() has changed to“~/.virtualenvs/iRfcb”..adc file format (IFCB1-6) byargumentold_adc in:ifcb_extract_pngs()ifcb_extract_classified_images()ifcb_extract_annotated_images()ifcb_read_mat() now returns consistent data structuresaligned withR.matlab::readMat() (#50).ifcb_summarize_png_data() is now defunct (previouslydeprecated in version 0.3.11).adc_folder inifcb_annotate_batch()(replaced byadc_files).unclassified_id inifcb_create_empty_manual_file() (replaced byclasslist).utm_zone inifcb_is_near_land() (nowdetermined automatically from longitude).ifcb_create_empty_manual_file() now accepts a completeclass list viaclasslist, replacing the olderunclassified_id.ifcb_summarize_biovolumes() now handles custom classlists.fs andshinytest.imager (replaced bypng) inifcb_extract_pngs() andbase64encdependencies.gamma argument toifcb_extract_pngs().verbose argument to functions:ifcb_download_test_data()ifcb_extract_biovolumes()ifcb_is_diatom()ifcb_read_features()ifcb_summarize_biovolumes()iRfcb:::retrieve_worms_records()) to top-level function:ifcb_match_taxa_names().ifcb_get_ferrybox_data() where multipleclose ferrybox timestamps caused duplicate rows. Now returns only thenearest match.ifcb_get_shark_example() andifcb_get_shark_colnames() for testing anddocumentation.ifcb_merge_manual() to merge manual.mat datasets.ifcb_adjust_classes() to adjust classes in manualdata.ifcb_create_class2use() to generate a class2usefile.ifcb_create_empty_manual_file() to create newmanual.mat files.ifcb_annotate_batch() to annotate multiple.mat files in a batch based on.pngimages..mat files to save space usingdo_compression argument in:ifcb_correct_annotation()ifcb_replace_mat_values()ifcb_summarize_png_metadata() to summarizeEcoTaxa metadata.ifcb_get_ecotaxa_example() to extract EcoTaxaheaders and example data.iRfcb:::split_large_zip() inifcb_zip_pngs().ifcb_summarize_png_data() (replaced byifcb_summarize_png_counts()).ifcb_get_svea_position().iRfcb:::handle_missing_positions().manual_folder,feature_folder, andclass_folder in severalfunctions (ifcb_count_mat_annotations(),ifcb_extract_biovolumes(),ifcb_read_features(),ifcb_summarize_biovolumes().nrow(taxa_list) == 0 inifcb_count_mat_annotations().mat_recursive option toifcb_count_mat_annotations().manual_recursive option toifcb_extract_annotated_images() andifcb_zip_matlab().roi_recursive option toifcb_extract_annotated_images().data_recursive option toifcb_zip_matlab().feature_recursive option toifcb_zip_matlab().marine_only toifcb_is_diatom(),iRfcb:::retrieve_worms_records(),ifcb_summarize_biovolumes() andifcb_extract_biovolumes().feature_recursive toifcb_extract_biovolumes() andifcb_summarize_biovolumes().mat_recursive toifcb_extract_biovolumes() andifcb_summarize_biovolumes().hdr_recursive toifcb_summarize_biovolumes().ifcb_is_diatom().ifcb_summarize_biovolumes().ifcb_is_in_basin().ifcb_get_shark_example() andifcb_get_shark_colnames().iRfcb:::retrieve_worms_records().ifcb_get_svea_position() (replaced byifcb_get_ferrybox_data()).ifcb_summarize_biovolumes().sleep_time parameter forifcb_download_test_data()..mat count edge case.curl for downloads.ifcb_psd() withargumentmicron_factor.testthat for improvestability.verbose argument to several functions to providedetailed progress messages during execution.ifcb_replace_mat_values() now only handles.mat files in themanual_folder.ifcb_is_near_land() now returnsNA ifcoordinates passed to the function containNA values.ifcb_get_trophic_type() to assign trophicstrategy to taxa.ifcb_get_shark_colnames():WADEP,PDMET,METFP,IFCBNO,TRPHY,ABUND, andBIOVOL.SAMPLE_TIME,ABUND_UNITS_PER_LITER,BIOVOL_PER_SAMPLE,BIOVOL_PER_LITER,C_CONC_PER_LITER, andSEA_BASIN.extract_aphia_id(): Extract AphiaID from WoRMSrecord.extract_class(): Extract taxonomic class from WoRMSrecord.handle_missing_positions(): Handle missing positions byrounding timestamps.ifcb_extract_biovolumes(): Compute biovolumes andcarbon from IFCB data.ifcb_get_shark_colnames(): Retrieve column names forSHARK submission.ifcb_get_svea_position(): Extract GPS coordinates fromferrybox data.ifcb_is_diatom(): Identify diatoms in a taxa list.ifcb_is_in_basin(): Check whether points fall inside asea basin.ifcb_psd_plot(): Create particle size distributionplots from IFCB data.ifcb_read_features(): Read IFCB feature files from aspecified folder.ifcb_summarize_biovolumes(): Summarize biovolumes andcarbon content.ifcb_summarize_class_counts(): Count TreeBaggerclassifier outputs.ifcb_which_basin(): Return name of sea basin a pointbelongs to.summarize_TBclass(): Summarize TreeBagger classifierresults.vol2C_lgdiatom(): Convert biovolume to carbon for largediatoms.vol2C_nondiatom(): Convert biovolume to carbon fornon-diatom protists.ifcb_read_hdr_data() wheregps_only filtering could fail.ifcb_volume_analyzed() wheninhibitiontime == 0 (#2).ifcb_is_near_land() by applyingsf::st_wrap_dateline() only when the CRS isgeographic.Initial development release ofiRfcb.
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()