Accessing and Validating Marine Environmental Data from 'SHARK' and Related Databases
Read SHARK Excel delivery files (.xls or .xlsx)
Read SHARK export files (tab- or semicolon-delimited, plain text or zi...
Launch the SHARK4R Bio-QC Tool
Match Dyntaxa taxon names
Taxon matching using Dyntaxa (https://www.dyntaxa.se/)
Match station names against SMHI station list
Match Dyntaxa taxon names
Retrieve WoRMS records by taxonomic names with retry logic
Taxon matching using WoRMS (http://www.marinespecies.org/)
Check if stations are reported as nominal positions
Parse scientific names into genus and species components.
Create a Leaflet map.
Create an interactive Leaflet map of sampling stations
Determine if positions are near land
Lookup spatial information for geographic points
Search AlgaeBase for information about a genus of algae
Search AlgaeBase for information about a species of algae
Search AlgaeBase for taxonomic information
Search AlgaeBase for taxonomic information
Read a Plankton Toolbox export file
Add WoRMS taxonomy hierarchy to AphiaIDs or scientific names
Assign phytoplankton group to scientific names
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Check if the required and recommended datatype-specific SHARK system f...
Uses data from national marine monitoring for the last 5 years to iden...
Check if the required and recommended datatype-specific SHARK system f...
Check matches of reported codes in SMHI's SHARK codelist
Check matches of reported codes in SMHI's SHARK codelist
Validate SHARK system fields in a data frame
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Validate depth values against bathymetry and logical constraints
Check if Abundance class exceeds 10
Uses data from national marine monitoring for the last 5 years to iden...
Check if Epibenthos cover exceeds 100%
Check if Epibenthos cover class exceeds 10
Check if Epibenthos cover (%) exceeds 100%
Uses data from national marine monitoring for the last 5 years to iden...
Check if Sediment deposition cover (%) exceeds 100%
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Check if Epibenthos total cover exceeds 100%
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Validate SHARK data fields for a given datatype
Uses data from national marine monitoring for the last 5 years to iden...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Uses data from national marine monitoring for the last 5 years to iden...
Check if the required and recommended datatype-specific SHARK system f...
Uses data from national marine monitoring for the last 5 years to iden...
General checker for parameter-specific logical rules
Check if stations are reported as nominal positions
Check whether points are located on land
General outlier check function for SHARK data
Check parameter values against logical rules
Check if the required and recommended datatype-specific SHARK system f...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Check if the required and recommended datatype-specific SHARK system f...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Check if the required and recommended datatype-specific SHARK system f...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Check if the required and recommended datatype-specific SHARK system f...
Uses data from national marine monitoring for the last 5 years to iden...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Check if the required and recommended datatype-specific SHARK system f...
Download and set up SHARK4R support files
Check station distances against SMHI station list
Identify non-numeric or non-logical values in measurement data
Identify samples with zero-valued station coordinates
Identify records with zero-valued measurement data
Uses data from national marine monitoring for the last 5 years to iden...
Check logical relationship between Abundance and BQIm
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Check if wet weight measurements are zero
Uses data from national marine monitoring for the last 5 years to iden...
Check if the required and recommended datatype-specific SHARK system f...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Uses data from national marine monitoring for the last 5 years to iden...
Check if the required and recommended datatype-specific SHARK system f...
Clean SHARK4R cache by file age and session
Construct a hierarchical taxonomy table from Dyntaxa
Convert coordinates from DDMM format to decimal degrees
Defunct functions
Find required fields in a SHARK delivery template
Search AlgaeBase for information about a genus of algae
Search AlgaeBase for information about a species of algae
Get a delivery template for a SHARK datatype
Download and read Darwin Core Archive files from Dyntaxa
Get parent taxon IDs for specified taxon IDs from Dyntaxa
Get taxonomic information from Dyntaxa for specified taxon IDs
Download the IOC-UNESCO Taxonomic Reference List of Harmful Micro Alga...
Get the latest NOMP biovolume Excel list
Retrieve external links or facts for taxa from Nordic Microalgae
Retrieve harmfulness for taxa from Nordic Microalgae
Retrieve and extract media URLs from Nordic Microalgae
Retrieve taxa information from Nordic Microalgae
Get the latest EG-Phyto/PEG biovolume Excel list
Get SHARK codelist from SMHI
Retrieve tabular data from SHARK
Download SHARK dataset zip archives
Retrieve available search options from SHARK
Summarize numeric SHARK parameters with ranges and outlier thresholds
Retrieve SHARK data table row counts
Retrieve marine biotoxin data from IOC-UNESCO Toxins Database
Retrieve hierarchical classification from WoRMS
Retrieve WoRMS records by taxonomic names with retry logic
Retrieve WoRMS records
Retrieve hierarchical taxonomy data from WoRMS
Determine if positions are near land
Determine if points are in a specified sea basin
Check if taxon names exist in Dyntaxa
Load SHARK4R fields from GitHub
Load SHARK4R statistics from GitHub
Load station database (station.txt) from path, NODC_CONFIG, or package...
Scatterplot with optional horizontal threshold lines
Read .xls files delivered to SHARK
Read .xlsx files delivered to SHARK
Read zip archive and unzip tab delimited files downloaded from SHARK
Read tab delimited files downloaded from SHARK
SHARK4R: Accessing and Validating Marine Environmental Data from 'SHAR...
Translate SHARK4R datatype names
Update SHARK taxonomy records using Dyntaxa
Retrieve and organize WoRMS taxonomy for SHARK Aphia IDs
Determine if points are in a specified sea basin
Provides functions to retrieve, process, analyze, and quality-control marine physical, chemical, and biological data. The main focus is on Swedish monitoring data available through the 'SHARK' database <https://shark.smhi.se/en/>, with additional API support for 'Nordic Microalgae' <https://nordicmicroalgae.org/>, 'Dyntaxa' <https://artfakta.se/>, World Register of Marine Species ('WoRMS') <https://www.marinespecies.org>, 'AlgaeBase' <https://www.algaebase.org>, OBIS 'xylookup' web service <https://iobis.github.io/xylookup/> and Intergovernmental Oceanographic Commission (IOC) - UNESCO databases on harmful algae <https://www.marinespecies.org/hab/> and toxins <https://toxins.hais.ioc-unesco.org/>.
Useful links