Package: iRfcb
Type: Package
Title: Tools for Managing Imaging FlowCytobot (IFCB) Data
Version: 0.4.3
Authors@R: c(
    person("Anders", "Torstensson", email = "anders.torstensson@smhi.se", role = c("aut", "cre"),
           comment = c(affiliation = "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 = c(funding = "Horizon Europe, HORIZON-MISS-2022-OCEAN-01-07"))
  )
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/>, 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
Encoding: UTF-8
Imports: zip, lifecycle, shiny, stringr, dplyr, sf, reticulate (>=
        1.41.0), tidyr, ggplot2, readr, worrms, png, R.matlab, curl,
        lubridate
RoxygenNote: 7.3.2
Note: This package includes code from https://github.com/kudelalab/PSD
        by kudelalab licensed under the MIT License.
Suggests: knitr, rmarkdown, testthat (>= 3.0.0), fs, mockery,
        shinytest2
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://europeanifcbgroup.github.io/iRfcb/,
        https://github.com/EuropeanIFCBGroup/iRfcb
NeedsCompilation: no
Packaged: 2025-03-13 22:12:00 UTC; anderstorstensson
Author: Anders Torstensson [aut, cre] (Swedish Meteorological and Hydrological
    Institute, <https://orcid.org/0000-0002-8283-656X>),
  Kendra Hayashi [ctb] (<https://orcid.org/0000-0003-1600-9504>),
  Jamie Enslein [ctb],
  Raphael Kudela [ctb] (<https://orcid.org/0000-0002-8640-1205>),
  Alle Lie [ctb] (<https://orcid.org/0009-0001-8709-4841>),
  Jayme Smith [ctb] (<https://orcid.org/0000-0002-9669-4427>),
  DTO-BioFlow [fnd] (Horizon Europe, HORIZON-MISS-2022-OCEAN-01-07)
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Repository: CRAN
Date/Publication: 2025-03-15 17:20:01 UTC
Built: R 4.6.0; ; 2025-04-15 03:22:52 UTC; windows
