Package index • iRfcb

Main functions

ifcb_adjust_classes(): Adjust Classifications in Manual Annotations

ifcb_annotate_batch(): Annotate IFCB Images with Specified Class

ifcb_convert_filenames(): Convert IFCB Filenames to Timestamps

ifcb_correct_annotation(): Correct Annotations in MATLAB Classlist Files

ifcb_count_mat_annotations(): Count IFCB Annotations from .mat Files

ifcb_create_class2use(): Create a class2use .mat File

ifcb_create_empty_manual_file(): Create an Empty Manual Classification MAT File

ifcb_create_manifest(): Create a MANIFEST.txt File

ifcb_download_test_data(): Download Test IFCB 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_match_taxa_names(): Retrieve WoRMS Records with Retry Mechanism

ifcb_merge_manual(): Merge IFCB Manual Classification Data

ifcb_psd(): Plot and Save IFCB PSD Data

ifcb_psd_plot(): Generate PSD Plot for a Given Sample

ifcb_py_install(): Install iRfcb Python Environment

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_replace_mat_values(): Replace Values in MATLAB Classlist

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_data() deprecated: 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

Helper functions

check_python_and_module(): Check Python and Required Modules Availability

create_package_manifest(): Function to Create MANIFEST.txt

.onLoad(): Load iRfcb Python Environment on Package Load

extract_aphia_id(): Extract the AphiaID from the First Row of Each worms_records Tibble

extract_class(): Extract the Class from the First Row of Each worms_records Tibble

extract_features(): Extract Features and Add Sample Names

extract_parts(): Function to Extract Parts Using Regular Expressions

find_matching_data(): Function to Find Matching Data Files with a General Pattern

find_matching_features(): Function to Find Matching Feature Files with a General Pattern

handle_missing_ferrybox_data(): Handle Missing Ferrybox Data

print_progress(): Function to Print the Progress Bar

read_hdr_file(): Function to Read Individual Files and Extract Relevant Lines

retrieve_worms_records() deprecated: Retrieve WoRMS Records with Retry Mechanism

split_large_zip(): Split Large Zip File into Smaller Parts

summarize_TBclass(): Summarize TreeBagger Classifier Results

truncate_folder_name(): Function to Truncate the Folder Name

vol2C_lgdiatom(): Convert Biovolume to Carbon for Large Diatoms

vol2C_nondiatom(): Convert Biovolume to Carbon for Non-Diatom Protists