Type: Package
Package: iRfcb
Title: Tools for Managing Imaging FlowCytobot (IFCB) Data
Version: 0.9.0.9000
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, readr, reticulate (>= 1.41.0), sf, shiny, stringr, tidyr,
        worrms, zip, jsonlite
Suggests: hdf5r, knitr, mockery, R.matlab, 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.
Roxygen: list(markdown = TRUE)
Config/Needs/website: rmarkdown
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev
        make libicu-dev libpng-dev libuv1-dev libssl-dev libproj-dev
        python3 libsqlite3-dev libudunits2-dev libx11-dev zlib1g-dev
Repository: https://europeanifcbgroup.r-universe.dev
Date/Publication: 2026-07-01 11:38:05 UTC
RemoteUrl: https://github.com/europeanifcbgroup/irfcb
RemoteRef: HEAD
RemoteSha: b48fd7db6048d7711c4da39808c9fe7aa1258870
NeedsCompilation: no
Packaged: 2026-07-01 12:36:32 UTC; root
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>