Package: iRfcb 0.4.3
Anders Torstensson
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.
Authors:
iRfcb_0.4.3.tar.gz
iRfcb_0.4.3.tar.gz(r-4.5-noble)iRfcb_0.4.3.tar.gz(r-4.4-noble)
iRfcb_0.4.3.tgz(r-4.4-emscripten)iRfcb_0.4.3.tgz(r-4.3-emscripten)
iRfcb.pdf |iRfcb.html✨
iRfcb/json (API)
| # Install 'iRfcb' in R: |
| install.packages('iRfcb', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/europeanifcbgroup/irfcb/issues
Pkgdown site:https://europeanifcbgroup.github.io
Last updated 10 hours agofrom:e3ae5d50dd. Checks:3 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 15 2025 |
| R-4.5-linux | OK | Mar 15 2025 |
| R-4.4-linux | OK | Mar 15 2025 |
Exports:create_package_manifestifcb_adjust_classesifcb_annotate_batchifcb_convert_filenamesifcb_correct_annotationifcb_count_mat_annotationsifcb_create_class2useifcb_create_empty_manual_fileifcb_create_manifestifcb_download_test_dataifcb_extract_annotated_imagesifcb_extract_biovolumesifcb_extract_classified_imagesifcb_extract_pngsifcb_get_ecotaxa_exampleifcb_get_ferrybox_dataifcb_get_mat_namesifcb_get_mat_variableifcb_get_runtimeifcb_get_shark_colnamesifcb_get_shark_exampleifcb_get_trophic_typeifcb_is_diatomifcb_is_in_basinifcb_is_near_landifcb_match_taxa_namesifcb_merge_manualifcb_psdifcb_psd_plotifcb_py_installifcb_read_featuresifcb_read_hdr_dataifcb_read_matifcb_read_summaryifcb_replace_mat_valuesifcb_run_image_galleryifcb_summarize_biovolumesifcb_summarize_class_countsifcb_summarize_png_countsifcb_summarize_png_dataifcb_summarize_png_metadataifcb_volume_analyzedifcb_volume_analyzed_from_adcifcb_which_basinifcb_zip_matlabifcb_zip_pngsread_hdr_fileretrieve_worms_recordssplit_large_zipsummarize_TBclassvol2C_lgdiatomvol2C_nondiatom
Dependencies:base64encbitbit64bslibcachemclassclassIntclicliprcolorspacecommonmarkcpp11crayoncrulcurldata.tableDBIdigestdplyre1071fansifarverfastmapfontawesomefsgenericsggplot2gluegtableherehmshtmltoolshttpcodehttpuvisobandjquerylibjsonliteKernSmoothlabelinglaterlatticelifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellnlmepillarpkgconfigpngprettyunitsprogresspromisesproxypurrrR.matlabR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppTOMLreadrreticulaterlangrprojroots2sassscalessfshinysourcetoolsstringistringrtibbletidyrtidyselecttimechangetriebeardtzdbunitsurltoolsutf8vctrsviridisLitevroomwithrwkworrmsxtablezip
Handling MATLAB Results
Rendered frommatlab-tutorial.Rmdusingknitr::rmarkdownon Mar 15 2025.Last update: 2025-03-15
Started: 2025-03-15
iRfcb Introduction
Rendered froma-general-tutorial.Rmdusingknitr::rmarkdownon Mar 15 2025.Last update: 2025-03-15
Started: 2025-03-15
Prepare IFCB Images for EcoTaxa
Rendered fromecotaxa-tutorial.Rmdusingknitr::rmarkdownon Mar 15 2025.Last update: 2025-03-15
Started: 2025-03-15
Quality Control of IFCB Data
Rendered fromqc-tutorial.Rmdusingknitr::rmarkdownon Mar 15 2025.Last update: 2025-03-15
Started: 2025-03-15
Sharing Annotated IFCB Images
Rendered fromimage-export-tutorial.Rmdusingknitr::rmarkdownon Mar 15 2025.Last update: 2025-03-15
Started: 2025-03-15
