Package: iRfcb 0.4.3.9000

Anders Torstensson

iRfcb: Tools for Managing Imaging FlowCytobot (IFCB) Data

A comprehensive suite of tools for managing, processing, and analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports quality control, geospatial analysis, and preparation of IFCB data for publication in databases like <https://www.gbif.org>, <https://www.obis.org>, <https://emodnet.ec.europa.eu/en>, <https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package integrates with the MATLAB 'ifcb-analysis' tool, which is described in Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides features for working with raw, manually classified, and machine learning–classified image datasets. Key functionalities include image extraction, particle size distribution analysis, taxonomic data handling, and biomass concentration calculations, essential for plankton research.

Authors:Anders Torstensson [aut, cre], Kendra Hayashi [ctb], Jamie Enslein [ctb], Raphael Kudela [ctb], Alle Lie [ctb], Jayme Smith [ctb], DTO-BioFlow [fnd]

iRfcb_0.4.3.9000.tar.gz
iRfcb_0.4.3.9000.zip(r-4.5)iRfcb_0.4.3.9000.zip(r-4.4)iRfcb_0.4.3.9000.zip(r-4.3)
iRfcb_0.4.3.9000.tgz(r-4.5-any)iRfcb_0.4.3.9000.tgz(r-4.4-any)iRfcb_0.4.3.9000.tgz(r-4.3-any)
iRfcb_0.4.3.9000.tar.gz(r-4.5-noble)iRfcb_0.4.3.9000.tar.gz(r-4.4-noble)
iRfcb_0.4.3.9000.tgz(r-4.4-emscripten)iRfcb_0.4.3.9000.tgz(r-4.3-emscripten)
iRfcb.pdf |iRfcb.html✨
iRfcb/json (API)

# Install 'iRfcb' in R:
install.packages('iRfcb', repos = c('https://europeanifcbgroup.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/europeanifcbgroup/irfcb/issues

Pkgdown site:https://europeanifcbgroup.github.io

On CRAN:

Conda:

5.72 score 1 stars 52 exports 97 dependencies

Last updated 4 hours agofrom:39618fc68c. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 16 2025
R-4.5-winOKMar 16 2025
R-4.5-macOKMar 16 2025
R-4.5-linuxOKMar 16 2025
R-4.4-winOKMar 16 2025
R-4.4-macOKMar 16 2025
R-4.4-linuxOKMar 16 2025
R-4.3-winOKMar 16 2025
R-4.3-macOKMar 16 2025

Exports:create_package_manifestifcb_adjust_classesifcb_annotate_batchifcb_convert_filenamesifcb_correct_annotationifcb_count_mat_annotationsifcb_create_class2useifcb_create_empty_manual_fileifcb_create_manifestifcb_download_test_dataifcb_extract_annotated_imagesifcb_extract_biovolumesifcb_extract_classified_imagesifcb_extract_pngsifcb_get_ecotaxa_exampleifcb_get_ferrybox_dataifcb_get_mat_namesifcb_get_mat_variableifcb_get_runtimeifcb_get_shark_colnamesifcb_get_shark_exampleifcb_get_trophic_typeifcb_is_diatomifcb_is_in_basinifcb_is_near_landifcb_match_taxa_namesifcb_merge_manualifcb_psdifcb_psd_plotifcb_py_installifcb_read_featuresifcb_read_hdr_dataifcb_read_matifcb_read_summaryifcb_replace_mat_valuesifcb_run_image_galleryifcb_summarize_biovolumesifcb_summarize_class_countsifcb_summarize_png_countsifcb_summarize_png_dataifcb_summarize_png_metadataifcb_volume_analyzedifcb_volume_analyzed_from_adcifcb_which_basinifcb_zip_matlabifcb_zip_pngsread_hdr_fileretrieve_worms_recordssplit_large_zipsummarize_TBclassvol2C_lgdiatomvol2C_nondiatom

Dependencies:base64encbitbit64bslibcachemclassclassIntclicliprcolorspacecommonmarkcpp11crayoncrulcurldata.tableDBIdigestdplyre1071fansifarverfastmapfontawesomefsgenericsggplot2gluegtableherehmshtmltoolshttpcodehttpuvisobandjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigpngprettyunitsprogresspromisesproxypurrrR.matlabR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppTOMLreadrreticulaterlangrprojroots2sassscalessfshinysourcetoolsstringistringrtibbletidyrtidyselecttimechangetriebeardtzdbunitsurltoolsutf8vctrsviridisLitevroomwithrwkworrmsxtablezip

Handling MATLAB Results

Rendered frommatlab-tutorial.Rmdusingknitr::rmarkdownon Mar 16 2025.

Last update: 2025-03-14
Started: 2025-01-09

iRfcb Introduction

Rendered froma-general-tutorial.Rmdusingknitr::rmarkdownon Mar 16 2025.

Last update: 2025-03-05
Started: 2025-01-09

Prepare IFCB Images for EcoTaxa

Rendered fromecotaxa-tutorial.Rmdusingknitr::rmarkdownon Mar 16 2025.

Last update: 2025-03-14
Started: 2025-01-09

Quality Control of IFCB Data

Rendered fromqc-tutorial.Rmdusingknitr::rmarkdownon Mar 16 2025.

Last update: 2025-03-14
Started: 2025-01-09

Sharing Annotated IFCB Images

Rendered fromimage-export-tutorial.Rmdusingknitr::rmarkdownon Mar 16 2025.

Last update: 2025-03-14
Started: 2025-01-09

Readme and manuals

Help Manual

Help pageTopics
Function to Create MANIFEST.txtcreate_package_manifest
Adjust Classifications in Manual Annotationsifcb_adjust_classes
Annotate IFCB Images with Specified Classifcb_annotate_batch
Convert IFCB Filenames to Timestampsifcb_convert_filenames
Correct Annotations in MATLAB Classlist Filesifcb_correct_annotation
Count IFCB Annotations from .mat Filesifcb_count_mat_annotations
Create a class2use .mat Fileifcb_create_class2use
Create an Empty Manual Classification MAT Fileifcb_create_empty_manual_file
Create a MANIFEST.txt Fileifcb_create_manifest
Download Test IFCB Dataifcb_download_test_data
Extract Annotated Images from IFCB Dataifcb_extract_annotated_images
Extract Biovolumes from IFCB Data and Compute Carbon Contentifcb_extract_biovolumes
Extract Taxa Images from MATLAB Classified Sampleifcb_extract_classified_images
Extract Images from IFCB ROI Fileifcb_extract_pngs
Get Ecotaxa Column Namesifcb_get_ecotaxa_example
Retrieve Ferrybox Data for Specified Timestampsifcb_get_ferrybox_data
Get Variable Names from a MAT Fileifcb_get_mat_names
Get Classes from a MAT Fileifcb_get_mat_variable
Read IFCB Header File and Extract Runtime Informationifcb_get_runtime
Get Shark Column Namesifcb_get_shark_colnames
Get Shark Column Exampleifcb_get_shark_example
Get Trophic Type for a List of Plankton Taxaifcb_get_trophic_type
Identify Diatoms in Taxa Listifcb_is_diatom
Check if Points are in a Specific Sea Basinifcb_is_in_basin
Determine if Positions are Near Landifcb_is_near_land
Retrieve WoRMS Records with Retry Mechanismifcb_match_taxa_names
Merge IFCB Manual Classification Dataifcb_merge_manual
Plot and Save IFCB PSD Dataifcb_psd
Generate PSD Plot for a Given Sampleifcb_psd_plot
Install iRfcb Python Environmentifcb_py_install
Read Feature Files from a Specified Folder or File Pathsifcb_read_features
Reads HDR Data from IFCB HDR Filesifcb_read_hdr_data
Read a MATLAB .mat File in Rifcb_read_mat
Read and Summarize Classified IFCB Dataifcb_read_summary
Replace Values in MATLAB Classlistifcb_replace_mat_values
Run IFCB Image Galleryifcb_run_image_gallery
Summarize Biovolumes and Carbon Content from IFCB Dataifcb_summarize_biovolumes
Count Cells from TreeBagger Classifier Outputifcb_summarize_class_counts
Summarize Image Counts by Class and Sampleifcb_summarize_png_counts
Summarize PNG Image Metadataifcb_summarize_png_metadata
Estimate Volume Analyzed from IFCB Header Fileifcb_volume_analyzed
Estimate Volume Analyzed from IFCB ADC Fileifcb_volume_analyzed_from_adc
Determine if Points are in a Specified Sea Basinifcb_which_basin
Create a Zip Archive of Manual MATLAB Filesifcb_zip_matlab
Zip PNG Foldersifcb_zip_pngs
Function to Read Individual Files and Extract Relevant Linesread_hdr_file
Split Large Zip File into Smaller Partssplit_large_zip
Summarize TreeBagger Classifier Resultssummarize_TBclass
Convert Biovolume to Carbon for Large Diatomsvol2C_lgdiatom
Convert Biovolume to Carbon for Non-Diatom Protistsvol2C_nondiatom