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
 [aut, cre]
(Swedish Meteorological and Hydrological Institute),
Kendra Hayashi
[ctb],
Jamie Enslein [ctb],
Raphael Kudela
[ctb],
Alle Lie [ctb],
Jayme Smith [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: not available, r-oldrel: not available |
| 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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