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Retrieve Data

SHARK

These functions are used to retrieve and read data from SHARK

get_shark_options()
Retrieve available search options from SHARK
get_shark_codes()
Get SHARK codelist from SMHI
get_shark_data()
Retrieve tabular data from SHARK
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()
Read SHARK export files (tab- or semicolon-delimited, plain text or zipped)
read_shark_deliv()
Read SHARK Excel delivery files (.xls or .xlsx)

Dyntaxa

These functions are used to retrieve data from the Dyntaxa API

construct_dyntaxa_table()
Construct a hierarchical taxonomy table from Dyntaxa
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 Dyntaxa
get_dyntaxa_records()
Get taxonomic information from Dyntaxa for specified taxon IDs
is_in_dyntaxa()
Check if taxon names exist in Dyntaxa
match_dyntaxa_taxa()
Match Dyntaxa taxon names
update_dyntaxa_taxonomy()
Update SHARK taxonomy records using Dyntaxa

WoRMS

These functions are used to retrieve data from the WoRMS API

add_worms_taxonomy()
Add WoRMS taxonomy hierarchy to AphiaIDs or scientific names
assign_phytoplankton_group()
Assign phytoplankton group to scientific names
get_worms_classification()
Retrieve hierarchical classification from WoRMS
get_worms_records()
Retrieve WoRMS records
get_worms_taxonomy_tree()
Retrieve hierarchical taxonomy data from WoRMS
match_worms_taxa()
Retrieve WoRMS records by taxonomic names with retry logic

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 related to Plankton Toolbox

get_nomp_list()
Get the latest NOMP biovolume Excel list
get_peg_list()
Get the latest EG-Phyto/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()
Identify samples with zero-valued station coordinates
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()
Identify non-numeric or non-logical values in measurement data
check_zero_value()
Identify records with zero-valued measurement data
run_qc_app()
Launch the SHARK4R Bio-QC Tool

MISC

clean_shark4r_cache()
Clean SHARK4R cache by file age and session
convert_ddmm_to_dd()
Convert coordinates from DDMM format to decimal degrees
find_required_fields()
Find required fields in a SHARK delivery template
get_delivery_template()
Get a delivery template for a SHARK datatype
load_shark4r_stats()
Load SHARK4R statistics from GitHub
load_shark4r_fields()
Load SHARK4R fields from GitHub
scatterplot()
Scatterplot with optional horizontal threshold lines
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
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