Package index • SHARK4R

Retrieve Data

SHARK

These functions are used to retrieve and read data from SHARK

get_shark_options(): Retrieve available search options from SHARK API

get_shark_codes(): Get SHARK codelist from SMHI

get_shark_data(): Retrieve data from the SHARK API

get_shark_datasets(): Download SHARK dataset zip archives

get_shark_statistics(): Summarize numeric SHARK parameters with ranges and outlier thresholds

get_shark_table_counts(): Retrieve SHARK data table row counts

read_shark_deliv(): Read SHARK Excel delivery files (.xls or .xlsx)

read_shark(): Read SHARK export files (tab- or semicolon-delimited, plain text or zipped)

Dyntaxa

These functions are used to retrieve data from the Dyntaxa API

construct_dyntaxa_table(): Construct Dyntaxa taxonomy table from API

get_dyntaxa_dwca(): Download and read Darwin Core Archive files from Dyntaxa

get_dyntaxa_parent_ids(): Get parent taxon IDs for specified taxon IDs from SLU Artdatabanken API (Dyntaxa)

get_dyntaxa_records(): Get taxonomic information from SLU Artdatabanken API for specified taxon IDs

is_in_dyntaxa(): Check if taxon names exist in Dyntaxa

match_dyntaxa_taxa(): Match Dyntaxa taxon names via API

update_dyntaxa_taxonomy(): Update taxonomy from SHARK via SLU Artdatabanken API (Dyntaxa)

WoRMS

These functions are used to retrieve data from the WoRMS API

add_worms_taxonomy(): Retrieve and organize WoRMS taxonomy for SHARK Aphia IDs

assign_phytoplankton_group(): Assign phytoplankton group to scientific names

get_worms_records(): Retrieve WoRMS records

match_worms_taxa(): Retrieve WoRMS records by taxonomic names with retry logic

match_worms_taxa_interactive(): Interactive taxon matching using WoRMS

AlgaeBase

These functions are used to retrieve data from the AlgaeBase API

match_algaebase_genus(): Search AlgaeBase for information about a genus of algae

match_algaebase_species(): Search AlgaeBase for information about a species of algae

match_algaebase_taxa(): Search AlgaeBase for taxonomic information

parse_scientific_names(): Parse scientific names into genus and species components.

IOC-UNESCO HAB

These functions are used to retrieve data from the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae and the IOC-UNESCO Toxins database.

get_hab_list(): Download the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae

get_toxin_list(): Retrieve marine biotoxin data from IOC-UNESCO Toxins Database

Nordic Microalgae

These functions are used to retrieve data from the Nordic Microalgae API

get_nua_external_links(): Retrieve external links or facts for taxa from Nordic Microalgae

get_nua_harmfulness(): Retrieve harmfulness for taxa from Nordic Microalgae

get_nua_media_links(): Retrieve and extract media URLs from Nordic Microalgae

get_nua_taxa(): Retrieve taxa information from Nordic Microalgae

Plankton Toolbox

These functions are used to read data exported from Plankton Toolbox

get_nomp_list(): Get the latest NOMP biovolume Excel list

get_peg_list(): Get PEG biovolume Excel list

read_ptbx(): Read a Plankton Toolbox export file

Quality Control

Geographical Data Checks

check_nominal_station(): Check if stations are reported as nominal positions

check_onland(): Check whether points are located on land

check_station_distance(): Check station distances against SMHI station list

check_zero_positions(): Check logical assumptions of data for station positions

lookup_xy(): Lookup spatial data for a set of points

match_station(): Match station names against SMHI station list

plot_map_leaflet(): Create an interactive Leaflet map of sampling stations

positions_are_near_land(): Determine if positions are near land

which_basin(): Determine if points are in a specified sea basin

SHARK Data Checks

check_codes(): Check matches of reported codes in SMHI's SHARK codelist

check_datatype(): Validate SHARK system fields in a data frame

check_depth(): Validate depth values against bathymetry and logical constraints

check_fields(): Validate SHARK data fields for a given datatype

check_logical_parameter(): General checker for parameter-specific logical rules

check_outliers(): General outlier check function for SHARK data

check_parameter_rules(): Check parameter values against logical rules

check_setup(): Download and set up SHARK4R support files

check_value_logical(): Check logical assumptions of data for specific variables and parameters

check_zero_value(): Check logical assumptions of data for specific variables and parameters

run_qc_app(): Launch the SHARK4R Bio-QC Tool

MISC

clean_shark4r_cache(): Clean SHARK4R cache by file age and session

find_required_fields(): Find required fields in a SHARK delivery template

get_delivery_template(): Get a delivery template for a SHARK datatype

scatterplot(): Interactive scatterplot with parameter selection and flexible axes

translate_shark_datatype(): Translate SHARK4R datatype names

Deprecated functions

check_Bacterioplankton() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_Chlorophyll() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_Epibenthos() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_EpibenthosDropvideo() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_GreySeal() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_HarbourPorpoise() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_HarbourSeal() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_PhysicalChemical() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_Phytoplankton() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_Picoplankton() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_PrimaryProduction() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_RingedSeal() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_SealPathology() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_Sedimentation() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_Zoobenthos() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_Zooplankton() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_bacterial_carbon() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_bacterial_concentration() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_bacterial_production() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_chlorophyll_conc() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_code_proj() deprecated: Check matches of reported codes in SMHI's SHARK codelist

check_deliv_Bacterioplankton() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_Chlorophyll() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_Epibenthos() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_EpibenthosDropvideo() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_GreySeal() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_HarbourPorpoise() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_HarbourSeal() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_PhysicalChemical() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_Phytoplankton() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_Picoplankton() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_PrimaryProduction() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_RingedSeal() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_SealPathology() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_Sedimentation() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_Zoobenthos() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_deliv_Zooplankton() deprecated: Check if the required and recommended datatype-specific SHARK system fields are present

check_epibenthos_abundclass_logical() deprecated: Check if Abundance class exceeds 10

check_epibenthos_counted() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_epibenthos_cover_logical() deprecated: Check if Epibenthos cover exceeds 100%

check_epibenthos_coverclass_logical() deprecated: Check if Epibenthos cover class exceeds 10

check_epibenthos_coverpercent_logical() deprecated: Check if Epibenthos cover (%) exceeds 100%

check_epibenthos_dryweight() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_epibenthos_sedimentdepos_logical() deprecated: Check if Sediment deposition cover (%) exceeds 100%

check_epibenthos_specdistr_maxdepth() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_epibenthos_specdistr_mindepth() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_epibenthos_totcover_logical() deprecated: Check if Epibenthos total cover exceeds 100%

check_greyseal_counted() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_harbourseal_counted() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_harbporp_positivemin() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_phytoplankton_abund() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_phytoplankton_biovol() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_phytoplankton_carbon() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_phytoplankton_counted() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_picoplankton_abundance() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_picoplankton_biovol() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_picoplankton_carbon() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_picoplankton_counted() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_primaryproduction_carbonprod() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_primaryproduction_carbonprod_hour() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_primaryproduction_carbonprodlight() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_ringedseal_calccounted() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zoobenthos_BQIm() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zoobenthos_BQIm_logical() deprecated: Check logical relationship between Abundance and BQIm

check_zoobenthos_abund() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zoobenthos_counted() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zoobenthos_wetweight() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zoobenthos_wetweight_logical() deprecated: Check if wet weight measurements are zero

check_zooplankton_abund() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zooplankton_carbon() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zooplankton_counted() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zooplankton_length_mean() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zooplankton_length_median() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zooplankton_wetweight() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zooplankton_wetweight_area() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

check_zooplankton_wetweight_volume() deprecated: Uses data from national marine monitoring for the last 5 years to identify outliers

get_algaebase_genus() deprecated: Search AlgaeBase for information about a genus of algae

get_algaebase_species() deprecated: Search AlgaeBase for information about a species of algae

get_worms_records_name() deprecated: Retrieve WoRMS records by taxonomic names with retry logic

ifcb_is_near_land() deprecated: Determine if positions are near land

ifcb_which_basin() deprecated: Determine if points are in a specified sea basin

match_algaebase() deprecated: Search AlgaeBase for taxonomic information

match_dyntaxa() deprecated: Taxon matching using Dyntaxa (https://www.dyntaxa.se/)

match_taxon_name() deprecated: Match Dyntaxa taxon names via API

match_wormstaxa() deprecated: Taxon matching using WoRMS (http://www.marinespecies.org/)

nominal_station() deprecated: Check if stations are reported as nominal positions

plot_map_leaflet_deliv() deprecated: Create a Leaflet map.

shark_read() deprecated: Read tab delimited files downloaded from SHARK

shark_read_deliv() deprecated: Read .xlsx files delivered to SHARK

shark_read_deliv_xls() deprecated: Read .xls files delivered to SHARK

shark_read_zip() deprecated: Read zip archive and unzip tab delimited files downloaded from SHARK

update_worms_taxonomy() deprecated: Retrieve and organize WoRMS taxonomy for SHARK Aphia IDs