# Tools for Managing Imaging FlowCytobot (IFCB) Data

## Documentation for package ‘iRfcb’ version 0.10.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

create_package_manifest | Function to Create MANIFEST.txt
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_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_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_manifest | Create a MANIFEST.txt File
ifcb_create_manual_file | Create a Manual Classification MAT 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 Classified Sample
ifcb_extract_features | Extract Slim Features and Blobs from IFCB Data
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_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_psd_plot | Generate PSD Plot for a Given Sample
ifcb_py_install | Install iRfcb Python Environment
ifcb_qc_sample | Quality-control a raw IFCB sample (hdr/adc/roi triplet)
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_mat | Read a MATLAB .mat File in R
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_save_classification | Classify an IFCB Sample and Save Results
ifcb_summarize_biovolumes | Summarize Biovolumes and Carbon Content from IFCB Data
ifcb_summarize_cell_counts | Summarize Diatom Cell Counts and Chain-Length Statistics 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_images_by_class | Zip Image Subfolders by Class
ifcb_zip_matlab | Create a Zip Archive of Manual MATLAB Files
ifcb_zip_pngs | Zip PNG Folders
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_diatom | Convert Biovolume to Carbon for Diatoms (All Sizes)
vol2C_diatom_auto | Convert Biovolume to Carbon for Diatoms, Choosing the Equation by Volume
vol2C_lgdiatom | Convert Biovolume to Carbon for Large Diatoms
vol2C_nondiatom | Convert Biovolume to Carbon for Non-Diatom Protists