Type: Package
Package: iRfcb
Title: Tools for Managing Imaging FlowCytobot (IFCB) Data
Version: 0.9.0
Authors@R: c(
    person("Anders", "Torstensson", email = "anders.torstensson@smhi.se", role = c("aut", "cre"),
           comment = c("Swedish Meteorological and Hydrological Institute", ORCID = "0000-0002-8283-656X")),
    person("Kendra", "Hayashi", role = "ctb",
           comment = c(ORCID = "0000-0003-1600-9504")),
    person("Jamie", "Enslein", role = "ctb"),
    person("Raphael", "Kudela", role = "ctb",
           comment = c(ORCID = "0000-0002-8640-1205")),
    person("Alle", "Lie", role = "ctb",
           comment = c(ORCID = "0009-0001-8709-4841")),
    person("Jayme", "Smith", role = "ctb",
           comment = c(ORCID = "0000-0002-9669-4427")),
    person("DTO-BioFlow", role = "fnd",
           comment = "Horizon Europe, HORIZON-MISS-2022-OCEAN-01-07"),
    person("SBDI", role = "fnd",
           comment = "Swedish Research Council, 2019-00242")
  )
Description: 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/en/>, 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.
License: MIT + file LICENSE
URL: https://europeanifcbgroup.github.io/iRfcb/,
        https://github.com/EuropeanIFCBGroup/iRfcb
Depends: R (>= 4.1)
Imports: cli, curl (>= 6.0.0), dplyr, ggplot2, lifecycle, lubridate,
        png, R.matlab, readr, reticulate (>= 1.41.0), sf, shiny,
        stringr, tidyr, worrms, zip, jsonlite
Suggests: hdf5r, knitr, mockery, rmarkdown, spelling, testthat (>=
        3.0.0)
Config/testthat/edition: 3
Config/testthat/parallel: true
Encoding: UTF-8
Language: en-US
Note: This package includes code from https://github.com/kudelalab/PSD
        by kudelalab licensed under the MIT License.
Config/Needs/website: rmarkdown
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
NeedsCompilation: no
Packaged: 2026-06-08 11:43:32 UTC; a002440
Author: Anders Torstensson [aut, cre] (Swedish Meteorological and Hydrological
    Institute, ORCID: <https://orcid.org/0000-0002-8283-656X>),
  Kendra Hayashi [ctb] (ORCID: <https://orcid.org/0000-0003-1600-9504>),
  Jamie Enslein [ctb],
  Raphael Kudela [ctb] (ORCID: <https://orcid.org/0000-0002-8640-1205>),
  Alle Lie [ctb] (ORCID: <https://orcid.org/0009-0001-8709-4841>),
  Jayme Smith [ctb] (ORCID: <https://orcid.org/0000-0002-9669-4427>),
  DTO-BioFlow [fnd] (Horizon Europe, HORIZON-MISS-2022-OCEAN-01-07),
  SBDI [fnd] (Swedish Research Council, 2019-00242)
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Repository: CRAN
Date/Publication: 2026-06-08 12:40:02 UTC
Built: R 4.6.0; ; 2026-06-08 15:11:45 UTC; unix
