Tools for Managing Imaging FlowCytobot (IFCB) Data

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Documentation for package ‘iRfcb’ version 0.5.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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_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_dashboard_data	Download IFCB data files from an IFCB Dashboard
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_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_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_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_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
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