Package index • iRfcb

Main functions

Functions for downloading IFCB data from dashboards and external repositories.

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_list_dashboard_bins(): Download bin list from the IFCB Dashboard API

Functions for reading raw IFCB files and extracting metadata.

ifcb_convert_filenames(): Convert IFCB Filenames to 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_read_features(): Read Feature Files from a Specified Folder or File Paths
ifcb_read_hdr_data(): Read Data from IFCB HDR Files
ifcb_read_summary(): Read and Summarize Classified IFCB Data
ifcb_volume_analyzed(): Estimate Volume Analyzed from IFCB Header File
ifcb_volume_analyzed_from_adc(): Estimate Volume Analyzed from IFCB ADC File

Functions for counting and summarizing annotated or classified images, biovolumes, and carbon content.

ifcb_count_mat_annotations(): Count IFCB Annotations from .mat Files
ifcb_extract_biovolumes(): Extract Biovolumes from IFCB Data and Compute Carbon Content
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

Functions for extracting images from raw IFCB .roi files.

ifcb_extract_annotated_images(): Extract Annotated Images from IFCB Data
ifcb_extract_classified_images(): Extract Taxa Images from Classified Sample
ifcb_extract_pngs(): Extract Images from IFCB ROI File

Functions for geospatial quality control and particle size distribution analysis.

Functions for taxonomic name matching, diatom classification, and trophic type lookup.

ifcb_get_trophic_type(): Get Trophic Type for a List of Plankton Taxa
ifcb_is_diatom(): Identify Diatoms in Taxa List
ifcb_match_taxa_names() superseded: Retrieve WoRMS Records with Retry Mechanism

Functions for packaging images and MATLAB files and preparing data for external repositories.

Functions for classifying IFCB images through a Gradio application.

ifcb_classify_images(): Classify Pre-Extracted IFCB PNG Images Using a Gradio Application
ifcb_classify_models(): List Available CNN Models from a Gradio Classification Server
ifcb_classify_sample(): Classify All Images in an IFCB Sample Using a Gradio Application
ifcb_save_classification(): Classify an IFCB Sample and Save Results

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_annotate_samples(): Create Manual Classification MAT Files from PNG Subfolders
ifcb_correct_annotation(): Correct Annotations in MATLAB Classlist Files
ifcb_create_class2use(): Create a class2use .mat File
ifcb_create_manual_file(): Create a 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

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

ifcb_create_empty_manual_file() deprecated: Create an Empty Manual Classification MAT File
retrieve_worms_records() deprecated: Retrieve WoRMS Records with Retry Mechanism
ifcb_run_image_gallery() deprecated: Run IFCB Image Gallery