Package index • SHARK4R

Retrieve Data

SHARK

These functions are used to retireve data from the SHARK API

get_shark_options(): Retrieve Available Search Options from SHARK API

get_shark_data(): Retrieve Data from SHARK API

get_shark_table_counts(): Retrieve SHARK Data Table Row Counts

Dyntaxa

These functions are used to retireve 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

match_taxon_name(): Match Dyntaxa taxon names via API

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

WoRMS

These functions are used to retireve 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

get_worms_records_name(): Retrieve WoRMS Records by Taxonomic Names with Retry Logic

AlgaeBase

These functions are used to retireve data from the AlgaeBase API

get_algaebase_genus(): Search AlgaeBase for Information About a Genus of Algae

get_algaebase_species(): Algaebase Species Search

match_algaebase(): Search Algaebase for Taxonomic Information

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

IOC-UNESCO HAB

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

get_hab_list(): Download the Harmful Algal Blooms (HABs) Taxonomic List

get_toxin_list(): Retrieve Toxin Data from IOC-UNESCO Toxins Database

Nordic Microalgae

These functions are used to retireve 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

Quality Control

Data Checks

check_Bacterioplankton(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_Chlorophyll(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_Epibenthos(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_EpibenthosDropvideo(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_GreySeal(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_HarbourPorpoise(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_HarbourSeal(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_PhysicalChemical(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_Phytoplankton(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_Picoplankton(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_PrimaryProduction(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_RingedSeal(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_SealPathology(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_Sedimentation(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_Zoobenthos(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_Zooplankton(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_bacterial_carbon(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_bacterial_concentration(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_bacterial_production(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_chlorophyll_conc(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_code_proj(): Check matches of reported project (PROJ) codes in SMHIs codelist

check_datatype(): Check if the required and recommended global and datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_Bacterioplankton(): Check if the required and recommended global and datatype-specific SHARK system fields (different between different datatypes) are present in intial deliveries of data (delivery validation).

check_deliv_Chlorophyll(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_Epibenthos(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_EpibenthosDropvideo(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_GreySeal(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_HarbourPorpoise(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_HarbourSeal(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_PhysicalChemical(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_Phytoplankton(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_Picoplankton(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_PrimaryProduction(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_RingedSeal(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_SealPathology(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_Sedimentation(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_Zoobenthos(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_deliv_Zooplankton(): Check if the required and recommended datatype-specific SHARK system fields (different between different datatypes) are present.

check_depth(): Check which points have potentially invalid depths.

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

check_epibenthos_counted(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

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

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

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

check_epibenthos_dryweight(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

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

check_epibenthos_specdistr_maxdepth(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_epibenthos_specdistr_mindepth(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

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

check_greyseal_counted(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_harbourseal_counted(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_harbporp_positivemin(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_onland(): Check which points are located on land.

check_phytoplankton_abund(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_phytoplankton_biovol(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_phytoplankton_carbon(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_picoplankton_abundance(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_picoplankton_biovol(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_picoplankton_carbon(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_picoplankton_counted(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_primaryproduction_carbonprod(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_primaryproduction_carbonprod_hour(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_primaryproduction_carbonprodlight(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_ringedseal_calccounted(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_station_distance(): Station distance check using SMHI station list "stations.txt" (the list is synced with "Stationsregistret": https://stationsregister.miljodatasamverkan.se/stationsregister/composer/) matches reported station name in data with curated station list and checks if it is within preset distance

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

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

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

check_zoobenthos_BQIm(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

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

check_zoobenthos_abund(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_zoobenthos_counted(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_zoobenthos_wetweight(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

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

check_zooplankton_abund(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_zooplankton_carbon(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_zooplankton_counted(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_zooplankton_length_mean(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_zooplankton_length_median(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_zooplankton_wetweight(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_zooplankton_wetweight_area(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

check_zooplankton_wetweight_volume(): Uses data from national marine monitoring for the last 5 years to identify outliers Ranges and IQR (interquantile range) for specific parameters is adapted to each datatype

ifcb_is_near_land(): Determine if Positions are Near Land

ifcb_which_basin(): Determine if Points are in a Specified Sea Basin

MISC

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

match_station(): Station matching using SMHI station list "stations.txt" (the list is synced with "Stationsregistret": https://stationsregister.miljodatasamverkan.se/stationsregister/composer/) matches reported station name in data with curated station list

match_wormstaxa(): Taxon matching using WoRMS (http://www.marinespecies.org/) matches latin name in data with WoRMS taxon list

nominal_station(): Check if stations are reported as nominal position or not Function makes an estimated guess whether stations are nominal

plot_map_leaflet(): Create a Leaflet map.

plot_map_leaflet_deliv(): Create a Leaflet map.

scatterplot(): Scatterplot of user-defined variables and parameters with x- and y-axes automatic selection Interactive plotly plot

shark_read(): Read tab delimited files downloaded from SHARK Uses read_delim to read tab delimited files with standardized export format from SHARK

shark_read_deliv(): Read .xlsx files delivered to SHARK Uses readxl to read excel files with standardized delivery format

shark_read_deliv_xls(): Read .xls files delivered to SHARK Uses readxl to read excel files with standardized delivery format

shark_read_zip(): Read zip archive and unzip tab delimited files downloaded from SHARK Uses unzip (unz) and read_delim to unzip archive and read tab delimited files with standardized export format from SHARK

Deprecated functions

get_shark_table() deprecated: Retrieve SHARK Table Data

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

update_worms_taxonomy() deprecated: Retrieve and Organize WoRMS Taxonomy for SHARK Aphia IDs