{
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  "Package": "SHARK4R",
  "Title": "Accessing and Validating Marine Environmental Data from 'SHARK'\nand Related Databases",
  "Version": "1.2.0",
  "Authors@R": "c(\nperson(\"Markus\", \"Lindh\", role = \"aut\",\ncomment = c(\"Swedish Meteorological and Hydrological Institute\", ORCID = \"0000-0002-7120-4145\")),\nperson(\"Anders\", \"Torstensson\", email = \"anders.torstensson@smhi.se\", role = c(\"aut\", \"cre\"),\ncomment = c(\"Swedish Meteorological and Hydrological Institute\", ORCID = \"0000-0002-8283-656X\")),\nperson(\"Mikael\", \"Hedblom\", role = \"ctb\",\ncomment = c(\"Swedish Meteorological and Hydrological Institute\", ORCID = \"0009-0007-5124-9956\")),\nperson(\"Bengt\", \"Karlson\", role = \"ctb\",\ncomment = c(\"Swedish Meteorological and Hydrological Institute\", ORCID = \"0000-0002-7524-3504\")),\nperson(\"Peter\", \"Thor\", role = \"ctb\",\ncomment = c(\"Swedish University of Agricultural Sciences\", ORCID = \"0000-0002-2603-2284\")),\nperson(\"Marie\", \"Johansen\", role = \"ctb\",\ncomment = c(\"Swedish Meteorological and Hydrological Institute\")),\nperson(\"SHARK\", email = \"shark@smhi.se\", role = \"cph\"),\nperson(\"SBDI\", role = \"fnd\",\ncomment = \"Swedish Research Council, 2019-00242\")\n)",
  "Description": "Provides functions to retrieve, process, analyze, and\nquality-control marine physical, chemical, and biological data.\nThe main focus is on Swedish monitoring data available through\nthe 'SHARK' database <https://shark.smhi.se/en/>, with\nadditional API support for 'Nordic Microalgae'\n<https://nordicmicroalgae.org/>, 'Dyntaxa'\n<https://artfakta.se/>, World Register of Marine Species\n('WoRMS') <https://www.marinespecies.org>, 'AlgaeBase'\n<https://www.algaebase.org>, OBIS 'xylookup' web service\n<https://iobis.github.io/xylookup/> and Intergovernmental\nOceanographic Commission (IOC) - UNESCO databases on harmful\nalgae <https://www.marinespecies.org/hab/> and toxins\n<https://toxins.hais.ioc-unesco.org/>.",
  "License": "MIT + file LICENSE",
  "URL": "https://sharksmhi.github.io/SHARK4R/,\nhttps://github.com/sharksmhi/SHARK4R",
  "BugReports": "https://github.com/sharksmhi/SHARK4R/issues",
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  "Repository": "https://sharksmhi.r-universe.dev",
  "Date/Publication": "2026-06-08 20:05:57 UTC",
  "RemoteUrl": "https://github.com/sharksmhi/shark4r",
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  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-08 20:27:36 UTC",
    "User": "root"
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  "Author": "Markus Lindh [aut] (Swedish Meteorological and Hydrological Institute,\nORCID: <https://orcid.org/0000-0002-7120-4145>),\nAnders Torstensson [aut, cre] (Swedish Meteorological and Hydrological\nInstitute, ORCID: <https://orcid.org/0000-0002-8283-656X>),\nMikael Hedblom [ctb] (Swedish Meteorological and Hydrological\nInstitute, ORCID: <https://orcid.org/0009-0007-5124-9956>),\nBengt Karlson [ctb] (Swedish Meteorological and Hydrological Institute,\nORCID: <https://orcid.org/0000-0002-7524-3504>),\nPeter Thor [ctb] (Swedish University of Agricultural Sciences, ORCID:\n<https://orcid.org/0000-0002-2603-2284>),\nMarie Johansen [ctb] (Swedish Meteorological and Hydrological\nInstitute),\nSHARK [cph],\nSBDI [fnd] (Swedish Research Council, 2019-00242)",
  "Maintainer": "Anders Torstensson <anders.torstensson@smhi.se>",
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  "_user": "sharksmhi",
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    "dyntaxa",
    "ioc-unesco",
    "nordicmicroalgae",
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    "quality-control",
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  "_exports": [
    "add_worms_taxonomy",
    "assign_phytoplankton_group",
    "calc_zooplankton_biomass",
    "calc_zooplankton_dry_weight",
    "check_bacterial_carbon",
    "check_bacterial_concentration",
    "check_bacterial_production",
    "check_Bacterioplankton",
    "check_Chlorophyll",
    "check_chlorophyll_conc",
    "check_code_proj",
    "check_codes",
    "check_datatype",
    "check_deliv_Bacterioplankton",
    "check_deliv_Chlorophyll",
    "check_deliv_Epibenthos",
    "check_deliv_EpibenthosDropvideo",
    "check_deliv_GreySeal",
    "check_deliv_HarbourPorpoise",
    "check_deliv_HarbourSeal",
    "check_deliv_PhysicalChemical",
    "check_deliv_Phytoplankton",
    "check_deliv_Picoplankton",
    "check_deliv_PrimaryProduction",
    "check_deliv_RingedSeal",
    "check_deliv_SealPathology",
    "check_deliv_Sedimentation",
    "check_deliv_Zoobenthos",
    "check_deliv_Zooplankton",
    "check_depth",
    "check_Epibenthos",
    "check_epibenthos_abundclass_logical",
    "check_epibenthos_counted",
    "check_epibenthos_cover_logical",
    "check_epibenthos_coverclass_logical",
    "check_epibenthos_coverpercent_logical",
    "check_epibenthos_dryweight",
    "check_epibenthos_sedimentdepos_logical",
    "check_epibenthos_specdistr_maxdepth",
    "check_epibenthos_specdistr_mindepth",
    "check_epibenthos_totcover_logical",
    "check_EpibenthosDropvideo",
    "check_fields",
    "check_GreySeal",
    "check_greyseal_counted",
    "check_HarbourPorpoise",
    "check_HarbourSeal",
    "check_harbourseal_counted",
    "check_harbporp_positivemin",
    "check_logical_parameter",
    "check_nominal_station",
    "check_onland",
    "check_outliers",
    "check_parameter_rules",
    "check_PhysicalChemical",
    "check_Phytoplankton",
    "check_phytoplankton_abund",
    "check_phytoplankton_biovol",
    "check_phytoplankton_carbon",
    "check_phytoplankton_counted",
    "check_Picoplankton",
    "check_picoplankton_abundance",
    "check_picoplankton_biovol",
    "check_picoplankton_carbon",
    "check_picoplankton_counted",
    "check_PrimaryProduction",
    "check_primaryproduction_carbonprod",
    "check_primaryproduction_carbonprod_hour",
    "check_primaryproduction_carbonprodlight",
    "check_RingedSeal",
    "check_ringedseal_calccounted",
    "check_SealPathology",
    "check_Sedimentation",
    "check_setup",
    "check_station_distance",
    "check_value_logical",
    "check_zero_positions",
    "check_zero_value",
    "check_Zoobenthos",
    "check_zoobenthos_abund",
    "check_zoobenthos_BQIm",
    "check_zoobenthos_BQIm_logical",
    "check_zoobenthos_counted",
    "check_zoobenthos_wetweight",
    "check_zoobenthos_wetweight_logical",
    "check_Zooplankton",
    "check_zooplankton_abund",
    "check_zooplankton_carbon",
    "check_zooplankton_counted",
    "check_zooplankton_length_mean",
    "check_zooplankton_length_median",
    "check_zooplankton_wetweight",
    "check_zooplankton_wetweight_area",
    "check_zooplankton_wetweight_volume",
    "clean_shark4r_cache",
    "construct_dyntaxa_table",
    "convert_ddmm_to_dd",
    "create_pie_map",
    "find_required_fields",
    "get_algaebase_genus",
    "get_algaebase_species",
    "get_delivery_template",
    "get_dyntaxa_dwca",
    "get_dyntaxa_parent_ids",
    "get_dyntaxa_records",
    "get_hab_list",
    "get_nomp_list",
    "get_nua_external_links",
    "get_nua_harmfulness",
    "get_nua_image_labeling_links",
    "get_nua_image_labeling_metadata",
    "get_nua_media_links",
    "get_nua_media_metadata",
    "get_nua_taxa",
    "get_peg_list",
    "get_shark_codes",
    "get_shark_data",
    "get_shark_datasets",
    "get_shark_options",
    "get_shark_statistics",
    "get_shark_table_counts",
    "get_toxin_list",
    "get_worms_classification",
    "get_worms_records",
    "get_worms_records_name",
    "get_worms_taxonomy_tree",
    "ifcb_is_near_land",
    "ifcb_which_basin",
    "is_in_dyntaxa",
    "load_shark4r_fields",
    "load_shark4r_stats",
    "lookup_xy",
    "match_algaebase",
    "match_algaebase_genus",
    "match_algaebase_species",
    "match_algaebase_taxa",
    "match_dyntaxa",
    "match_dyntaxa_taxa",
    "match_station",
    "match_taxon_name",
    "match_worms_taxa",
    "match_wormstaxa",
    "nominal_station",
    "parse_scientific_names",
    "plot_map_leaflet",
    "plot_map_leaflet_deliv",
    "positions_are_near_land",
    "read_ptbx",
    "read_shark",
    "read_shark_deliv",
    "run_qc_app",
    "scatterplot",
    "shark_read",
    "shark_read_deliv",
    "shark_read_deliv_xls",
    "shark_read_zip",
    "translate_shark_datatype",
    "update_dyntaxa_taxonomy",
    "update_worms_taxonomy",
    "which_basin"
  ],
  "_help": [
    {
      "page": "add_worms_taxonomy",
      "title": "Add WoRMS taxonomy hierarchy to AphiaIDs or scientific names",
      "topics": [
        "add_worms_taxonomy"
      ]
    },
    {
      "page": "assign_phytoplankton_group",
      "title": "Assign phytoplankton group to scientific names",
      "topics": [
        "assign_phytoplankton_group"
      ]
    },
    {
      "page": "calc_zooplankton_biomass",
      "title": "Calculate zooplankton biomass from dry weight and abundance",
      "topics": [
        "calc_zooplankton_biomass"
      ]
    },
    {
      "page": "calc_zooplankton_dry_weight",
      "title": "Calculate zooplankton dry weight from mean length",
      "topics": [
        "calc_zooplankton_dry_weight"
      ]
    },
    {
      "page": "check_codes",
      "title": "Check matches of reported codes in SMHI's SHARK codelist",
      "topics": [
        "check_codes"
      ]
    },
    {
      "page": "check_datatype",
      "title": "Validate SHARK system fields in a data frame",
      "topics": [
        "check_datatype"
      ]
    },
    {
      "page": "check_depth",
      "title": "Validate depth values against bathymetry and logical constraints",
      "topics": [
        "check_depth"
      ]
    },
    {
      "page": "check_fields",
      "title": "Validate SHARK data fields for a given datatype",
      "topics": [
        "check_fields"
      ]
    },
    {
      "page": "check_logical_parameter",
      "title": "General checker for parameter-specific logical rules",
      "topics": [
        "check_logical_parameter"
      ]
    },
    {
      "page": "check_nominal_station",
      "title": "Check if stations are reported as nominal positions",
      "topics": [
        "check_nominal_station"
      ]
    },
    {
      "page": "check_onland",
      "title": "Check whether points are located on land",
      "topics": [
        "check_onland"
      ]
    },
    {
      "page": "check_outliers",
      "title": "General outlier check function for SHARK data",
      "topics": [
        "check_outliers"
      ]
    },
    {
      "page": "check_parameter_rules",
      "title": "Check parameter values against logical rules",
      "topics": [
        "check_parameter_rules"
      ]
    },
    {
      "page": "check_setup",
      "title": "Download and set up SHARK4R support files",
      "topics": [
        "check_setup"
      ]
    },
    {
      "page": "check_station_distance",
      "title": "Check station distances against SMHI station list",
      "topics": [
        "check_station_distance"
      ]
    },
    {
      "page": "check_value_logical",
      "title": "Identify non-numeric or non-logical values in measurement data",
      "topics": [
        "check_value_logical"
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