Movatterモバイル変換

iRfcb 0.6.0

New features

• New functions for interacting with the IFCB Dashboard API:ifcb_download_dashboard_metadata() andifcb_list_dashboard_bins().
• Addeddiatom_include parameter toifcb_extract_biovolumes() andifcb_summarize_biovolumes() for manually forcing specifictaxa to be treated as diatoms (overrides WoRMS classification)(#65).
• Addedbins parameter toifcb_psd() forselecting which bins to process.
• Addedfea_v parameter toifcb_psd() forselecting feature-file version.
• Addeduse_plot_subfolders parameter toifcb_psd() to optionally save plots in subdirectories ofplot_folder based on flag status.
• Addedflags parameter toifcb_psd_plot()to optionally add the quality flag annotation to the plot.

Minor improvements and fixes

• 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.
• The$data,$fits and$flagsdata frames returned byifcb_psd() now use full bin names(<sample>_<ifcb>) as sample names, improvinguniqueness and consistency with downstream workflows.
• The$data and$fits data frames returnedbyifcb_psd() now preserves the original column names,including names starting with numbers or containing specialcharacters.
• Problematic character µ returned fromifcb_psd() hasbeen replaced by u in$data headers.
• Updated$flags headers inifcb_psd() tousesample instead offile, ensuringconsistent naming across all outputs.
• Reduced the size and resolution of saved plots inifcb_psd() whenplot_folder is specified,improving processing speed.

iRfcb 0.5.2

Minor improvements andfixes

• 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 zerobiovolume
• ifcb_read_features() andifcb_extract_biovolumes() now handles singlefeature_files correctly.
• Tests are now skipped if required resources are unavailable,improving stability in environments with limited access to externaldependencies.

iRfcb 0.5.1

Minor improvements andfixes

• Skipping certain internet-required tests on CRAN servers.
• Corrected help pages forifcb_download_dashboard_data()andifcb_download_whoi_plankton().

iRfcb 0.5.0

New features

• AddedNEWS.md to track package changes.
• New functions:
  • 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.
• New vignette:vignette("whoi-plankton-data-integration").
• Python virtual environments can now be automatically activated bysetting theUSE_IRFCB_PYTHON environment variable whenloading the package.
• Added scale bar support (#42) to:
  • ifcb_extract_pngs()
  • ifcb_extract_classified_images()
  • ifcb_extract_annotated_images()
• Addedgamma argument toifcb_extract_annotated_images () andifcb_extract_classified_images() for gamma correction.
• ifcb_is_near_land():
  • Now returns a plot ifplot = TRUE.
  • Added option to download EEA coastline data using the new argumentsource.
  • Deprecated the argumentutm_zone, which is nowdetermined automatically from longitude.

Minor improvements andfixes

• 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).
• The default location of the venv path inifcb_py_install() has changed to“~/.virtualenvs/iRfcb”.
• Added support for old.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).

Deprecations

• ifcb_summarize_png_data() is now defunct (previouslydeprecated in version 0.3.11).
• Deprecated arguments:
  • 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.

iRfcb 0.4.3

Minor improvements andfixes

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

iRfcb 0.4.2

Minor changes

• Updated documentation to pass CRAN checks.

iRfcb 0.4.1

Minor improvements andfixes

• Removedimager (replaced bypng) inifcb_extract_pngs() andbase64encdependencies.
• Addedgamma argument toifcb_extract_pngs().
• Updated vignettes.

iRfcb 0.4.0

New features

• Reorganized vignettes into multiple tutorials.
• Addedverbose 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 andfixes

• Fixed issue inifcb_get_ferrybox_data() where multipleclose ferrybox timestamps caused duplicate rows. Now returns only thenearest match.

iRfcb 0.3.14

Minor improvements andfixes

• Updated SHARK example inifcb_get_shark_example() andifcb_get_shark_colnames() for testing anddocumentation.

iRfcb 0.3.13

New features

• Addedifcb_merge_manual() to merge manual.mat datasets.
• Addedifcb_adjust_classes() to adjust classes in manualdata.
• Addedifcb_create_class2use() to generate a class2usefile.

iRfcb 0.3.12

New features

• Addedifcb_create_empty_manual_file() to create newmanual.mat files.
• Addedifcb_annotate_batch() to annotate multiple.mat files in a batch based on.pngimages.

Minor improvements andfixes

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

iRfcb 0.3.11

New features

• Addedifcb_summarize_png_metadata() to summarizeEcoTaxa metadata.
• Addedifcb_get_ecotaxa_example() to extract EcoTaxaheaders and example data.

Minor improvements andfixes

• Large ZIP files can now be split using helperiRfcb:::split_large_zip() inifcb_zip_pngs().

Deprecations

• Deprecatedifcb_summarize_png_data() (replaced byifcb_summarize_png_counts()).

iRfcb 0.3.10

Minor improvements andfixes

• Updated documentation and examples.

Deprecations

• Removed deprecated functionifcb_get_svea_position().
• Removed helperiRfcb:::handle_missing_positions().
• Deprecated argumentsmanual_folder,feature_folder, andclass_folder in severalfunctions (ifcb_count_mat_annotations(),ifcb_extract_biovolumes(),ifcb_read_features(),ifcb_summarize_biovolumes().

iRfcb 0.3.9

Minor improvements andfixes

• Fixed edge case wherenrow(taxa_list) == 0 inifcb_count_mat_annotations().
• Addedmat_recursive option toifcb_count_mat_annotations().
• Addedmanual_recursive option toifcb_extract_annotated_images() andifcb_zip_matlab().
• Addedroi_recursive option toifcb_extract_annotated_images().
• Addeddata_recursive option toifcb_zip_matlab().
• Addedfeature_recursive option toifcb_zip_matlab().

iRfcb 0.3.8

Minor improvements andfixes

• Addedmarine_only toifcb_is_diatom(),iRfcb:::retrieve_worms_records(),ifcb_summarize_biovolumes() andifcb_extract_biovolumes().
• Addedfeature_recursive toifcb_extract_biovolumes() andifcb_summarize_biovolumes().
• Addedmat_recursive toifcb_extract_biovolumes() andifcb_summarize_biovolumes().
• Addedhdr_recursive toifcb_summarize_biovolumes().
• Extracted helper function fromifcb_is_diatom().

iRfcb 0.3.7

New features

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

iRfcb 0.3.6

Minor improvements andfixes

• Removed Öresund from included Baltic Sea shape file used inifcb_is_in_basin().
• Updated SHARK column names for compatibility inifcb_get_shark_example() andifcb_get_shark_colnames().

iRfcb 0.3.5

Minor improvements andfixes

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

Deprecations

• Deprecatedifcb_get_svea_position() (replaced byifcb_get_ferrybox_data()).

iRfcb 0.3.4

Minor improvements andfixes

• Added option to summarize biovolumes from manual files inifcb_summarize_biovolumes().
• Addedsleep_time parameter forifcb_download_test_data().

iRfcb 0.3.3

Minor improvements andfixes

• Fixed manual.mat count edge case.
• Switched tocurl for downloads.
• Parameterized PSD micron factor inifcb_psd() withargumentmicron_factor.
• General clean-up of minor improvements and fixes.

iRfcb 0.3.2

Minor improvements andfixes

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

iRfcb 0.3.1

Minor improvements andfixes

• Corrected documentation errors.

iRfcb 0.3.0

New features

• Introduced unit testing withtestthat for improvestability.
• Improved consistency and functionality across multiplefunctions.

iRfcb 0.2.6

Minor improvements andfixes

• Minor update of documentation for clarity and consistency.

iRfcb 0.2.5

Minor improvements andfixes

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

iRfcb 0.2.4

Minor improvements andfixes

• Moved example documentation to vignettes.
• Addedverbose argument to several functions to providedetailed progress messages during execution.

iRfcb 0.2.3

Minor improvements andfixes

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

iRfcb 0.2.2

Minor improvements andfixes

• ifcb_is_near_land() now returnsNA ifcoordinates passed to the function containNA values.

iRfcb 0.2.1

New features

• Addedifcb_get_trophic_type() to assign trophicstrategy to taxa.

Minor improvements andfixes

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

iRfcb 0.2.0

New features

• New functions:
  • 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.

Minor improvements andfixes

• Fixed issue inifcb_read_hdr_data() wheregps_only filtering could fail.
• Extended tutorial to include examples using newly addedfunctions.

iRfcb 0.1.2

Minor improvements andfixes

• Fixed edge case inifcb_volume_analyzed() wheninhibitiontime == 0 (#2).

iRfcb 0.1.1

Minor improvements andfixes

• Fixed warning inifcb_is_near_land() by applyingsf::st_wrap_dateline() only when the CRS isgeographic.
• Updated function documentation for consistency.

iRfcb 0.1.0

Initial development release ofiRfcb.

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()