NEWS.md to track package changes.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.vignette("whoi-plankton-data-integration").USE_IRFCB_PYTHON environment variable when
loading the package.ifcb_extract_pngs()ifcb_extract_classified_images()ifcb_extract_annotated_images()gamma argument to
ifcb_extract_annotated_images () and
ifcb_extract_classified_images() for gamma correction.ifcb_is_near_land():
plot = TRUE.source.utm_zone, which is now
determined automatically from longitude.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).ifcb_py_install() has changed to
“~/.virtualenvs/iRfcb”..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).ifcb_summarize_png_data() is now defunct (previously
deprecated in version 0.3.11).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.ifcb_summarize_biovolumes() now handles custom class
lists.fs and
shinytest.imager (replaced by png) in
ifcb_extract_pngs() and base64enc
dependencies.gamma argument to
ifcb_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 multiple
close ferrybox timestamps caused duplicate rows. Now returns only the
nearest match.ifcb_get_shark_example() and
ifcb_get_shark_colnames() for testing and
documentation.ifcb_merge_manual() to merge manual
.mat datasets.ifcb_adjust_classes() to adjust classes in manual
data.ifcb_create_class2use() to generate a class2use
file.ifcb_create_empty_manual_file() to create new
manual .mat files.ifcb_annotate_batch() to annotate multiple
.mat files in a batch based on .png
images..mat files to save space using
do_compression argument in:
ifcb_correct_annotation()ifcb_replace_mat_values()ifcb_summarize_png_metadata() to summarize
EcoTaxa metadata.ifcb_get_ecotaxa_example() to extract EcoTaxa
headers and example data.iRfcb:::split_large_zip() in
ifcb_zip_pngs().ifcb_summarize_png_data() (replaced by
ifcb_summarize_png_counts()).ifcb_get_svea_position().iRfcb:::handle_missing_positions().manual_folder,
feature_folder, and class_folder in several
functions (ifcb_count_mat_annotations(),
ifcb_extract_biovolumes(),
ifcb_read_features(),
ifcb_summarize_biovolumes().nrow(taxa_list) == 0 in
ifcb_count_mat_annotations().mat_recursive option to
ifcb_count_mat_annotations().manual_recursive option to
ifcb_extract_annotated_images() and
ifcb_zip_matlab().roi_recursive option to
ifcb_extract_annotated_images().data_recursive option to
ifcb_zip_matlab().feature_recursive option to
ifcb_zip_matlab().marine_only to ifcb_is_diatom(),
iRfcb:::retrieve_worms_records(),
ifcb_summarize_biovolumes() and
ifcb_extract_biovolumes().feature_recursive to
ifcb_extract_biovolumes() and
ifcb_summarize_biovolumes().mat_recursive to
ifcb_extract_biovolumes() and
ifcb_summarize_biovolumes().hdr_recursive to
ifcb_summarize_biovolumes().ifcb_is_diatom().ifcb_summarize_biovolumes().ifcb_is_in_basin().ifcb_get_shark_example() and
ifcb_get_shark_colnames().iRfcb:::retrieve_worms_records().ifcb_get_svea_position() (replaced by
ifcb_get_ferrybox_data()).ifcb_summarize_biovolumes().sleep_time parameter for
ifcb_download_test_data()..mat count edge case.curl for downloads.ifcb_psd() with
argument micron_factor.testthat for improve
stability.verbose argument to several functions to provide
detailed progress messages during execution.ifcb_replace_mat_values() now only handles
.mat files in the manual_folder.ifcb_is_near_land() now returns NA if
coordinates passed to the function contain NA values.ifcb_get_trophic_type() to assign trophic
strategy to taxa.ifcb_get_shark_colnames():
WADEP, PDMET,
METFP, IFCBNO, TRPHY,
ABUND, and BIOVOL.SAMPLE_TIME,
ABUND_UNITS_PER_LITER, BIOVOL_PER_SAMPLE,
BIOVOL_PER_LITER, C_CONC_PER_LITER, and
SEA_BASIN.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.ifcb_read_hdr_data() where
gps_only filtering could fail.ifcb_volume_analyzed() when
inhibition time == 0 (#2).ifcb_is_near_land() by applying
sf::st_wrap_dateline() only when the CRS is
geographic.Initial development release of iRfcb.
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()