Package index • iRfcb

Main functions

Core functions

Core functions for processing and analyzing IFCB data.

ifcb_convert_filenames(): Convert IFCB Filenames to Timestamps
ifcb_count_mat_annotations(): Count IFCB Annotations from .mat Files
ifcb_create_manifest(): Create a MANIFEST.txt File
ifcb_download_dashboard_data(): Download IFCB data files from an IFCB Dashboard
ifcb_download_dashboard_metadata(): Download metadata from the IFCB Dashboard API
ifcb_download_test_data(): Download Test IFCB Data
ifcb_download_whoi_plankton(): Download and Extract WHOI-Plankton Data
ifcb_extract_annotated_images(): Extract Annotated Images from IFCB Data
ifcb_extract_biovolumes(): Extract Biovolumes from IFCB Data and Compute Carbon Content
ifcb_extract_classified_images(): Extract Taxa Images from MATLAB Classified Sample
ifcb_extract_pngs(): Extract Images from IFCB ROI File
ifcb_get_ecotaxa_example(): Get EcoTaxa Column Names
ifcb_get_ferrybox_data(): Retrieve Ferrybox Data for Specified Timestamps
ifcb_get_mat_names(): Get Variable Names from a MAT File
ifcb_get_mat_variable(): Get Classes from a MAT File
ifcb_get_runtime(): Read IFCB Header File and Extract Runtime Information
ifcb_get_shark_colnames(): Get Shark Column Names
ifcb_get_shark_example(): Get Shark Column Example
ifcb_get_trophic_type(): Get Trophic Type for a List of Plankton Taxa
ifcb_is_diatom(): Identify Diatoms in Taxa List
ifcb_is_in_basin(): Check if Points are in a Specific Sea Basin
ifcb_is_near_land(): Determine if Positions are Near Land
ifcb_list_dashboard_bins(): Download bin list from the IFCB Dashboard API
ifcb_match_taxa_names(): Retrieve WoRMS Records with Retry Mechanism
ifcb_psd_plot(): Generate PSD Plot for a Given Sample
ifcb_read_features(): Read Feature Files from a Specified Folder or File Paths
ifcb_read_hdr_data(): Reads HDR Data from IFCB HDR Files
ifcb_read_summary(): Read and Summarize Classified IFCB Data
ifcb_run_image_gallery(): Run IFCB Image Gallery
ifcb_summarize_biovolumes(): Summarize Biovolumes and Carbon Content from IFCB Data
ifcb_summarize_class_counts(): Count Cells from TreeBagger Classifier Output
ifcb_summarize_png_counts(): Summarize Image Counts by Class and Sample
ifcb_summarize_png_metadata(): Summarize PNG Image Metadata
ifcb_volume_analyzed(): Estimate Volume Analyzed from IFCB Header File
ifcb_volume_analyzed_from_adc(): Estimate Volume Analyzed from IFCB ADC File
ifcb_which_basin(): Determine if Points are in a Specified Sea Basin
ifcb_zip_matlab(): Create a Zip Archive of Manual MATLAB Files
ifcb_zip_pngs(): Zip PNG Folders

Python dependency

These functions depend on a working Python installation. For more information, see the README.

ifcb_adjust_classes(): Adjust Classifications in Manual Annotations
ifcb_annotate_batch(): Annotate IFCB Images with Specified Class
ifcb_correct_annotation(): Correct Annotations in MATLAB Classlist Files
ifcb_create_class2use(): Create a class2use .mat File
ifcb_create_empty_manual_file(): Create an Empty Manual Classification MAT File
ifcb_merge_manual(): Merge IFCB Manual Classification Data
ifcb_prepare_whoi_plankton(): Download and Prepare WHOI-Plankton Data
ifcb_psd(): Plot and Save IFCB PSD Data
ifcb_py_install(): Install iRfcb Python Environment
ifcb_replace_mat_values(): Replace Values in MATLAB Classlist
ifcb_read_mat(): Read a MATLAB .mat File in R

Helper functions

create_package_manifest(): Function to Create MANIFEST.txt
process_ifcb_string(): Process IFCB String
read_hdr_file(): Function to Read Individual Files and Extract Relevant Lines
split_large_zip(): Split Large Zip File into Smaller Parts
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

Deprecated functions

retrieve_worms_records() deprecated: Retrieve WoRMS Records with Retry Mechanism