Man pages for iRfcb
Tools for Managing Imaging FlowCytobot (IFCB) Data
| create_package_manifest | Function to Create MANIFEST.txt |
| defunct | Defunct 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_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 |
| iRfcb-package | iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data |
| process_ifcb_string | Process IFCB String |
| read_hdr_file | Function to Read Individual Files and Extract Relevant Lines |
| retrieve_worms_records | Retrieve WoRMS Records with Retry Mechanism |
| 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 |
