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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.

Version: 0.4.3
Imports: zip, lifecycle, shiny, stringr, dplyr, sf, reticulate (≥ 1.41.0), tidyr, ggplot2, readr, worrms, png, R.matlab, curl, lubridate
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0), fs, mockery, shinytest2
Published: 2025-03-15
DOI: 10.32614/CRAN.package.iRfcb
Author: Anders Torstensson ORCID iD [aut, cre] (Swedish Meteorological and Hydrological Institute), Kendra Hayashi ORCID iD [ctb], Jamie Enslein [ctb], Raphael Kudela ORCID iD [ctb], Alle Lie ORCID iD [ctb], Jayme Smith ORCID iD [ctb], DTO-BioFlow [fnd] (Horizon Europe, HORIZON-MISS-2022-OCEAN-01-07)
Maintainer: Anders Torstensson <anders.torstensson at smhi.se>
License: MIT + file LICENSE
URL: https://europeanifcbgroup.github.io/iRfcb/, https://github.com/EuropeanIFCBGroup/iRfcb
NeedsCompilation: no
Citation: iRfcb citation info
Materials: README
CRAN checks: iRfcb results

Documentation:

Reference manual: iRfcb.pdf
Vignettes: iRfcb Introduction (source, R code)
Prepare IFCB Images for EcoTaxa (source, R code)
Sharing Annotated IFCB Images (source, R code)
Handling MATLAB Results (source, R code)
Quality Control of IFCB Data (source, R code)

Downloads:

Package source: iRfcb_0.4.3.tar.gz
Windows binaries: r-devel: iRfcb_0.4.3.zip, r-release: iRfcb_0.4.3.zip, r-oldrel: iRfcb_0.4.3.zip
macOS binaries: r-devel (arm64): not available, r-release (arm64): not available, r-oldrel (arm64): not available, r-devel (x86_64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.