Accessing and Validating Marine Environmental Data from 'SHARK'
and Related Databases
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Documentation for package ‘SHARK4R’ version 1.0.3
Help Pages
| add_worms_taxonomy | Add WoRMS taxonomy hierarchy to AphiaIDs or scientific names |
| assign_phytoplankton_group | Assign phytoplankton group to scientific names |
| 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_nominal_station | Check if stations are reported as nominal positions |
| check_onland | Check whether points are located on land |
| 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_station_distance | Check station distances against SMHI station list |
| check_value_logical | Identify non-numeric or non-logical values in measurement data |
| check_zero_positions | Identify samples with zero-valued station coordinates |
| check_zero_value | Identify records with zero-valued measurement data |
| clean_shark4r_cache | Clean SHARK4R cache by file age and session |
| construct_dyntaxa_table | Construct a hierarchical taxonomy table from Dyntaxa |
| 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 |
| 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 |
| get_hab_list | Download the IOC-UNESCO Taxonomic Reference List of Harmful Micro Algae |
| get_nomp_list | Get the latest NOMP biovolume Excel list |
| 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 |
| get_peg_list | Get the latest EG-Phyto/PEG biovolume Excel list |
| 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_options | Retrieve available search options from SHARK |
| get_shark_statistics | Summarize numeric SHARK parameters with ranges and outlier thresholds |
| get_shark_table_counts | Retrieve SHARK data table row counts |
| get_toxin_list | Retrieve marine biotoxin data from IOC-UNESCO Toxins Database |
| get_worms_classification | Retrieve hierarchical classification from WoRMS |
| get_worms_records | Retrieve WoRMS records |
| get_worms_taxonomy_tree | Retrieve hierarchical taxonomy data from WoRMS |
| is_in_dyntaxa | Check if taxon names exist in Dyntaxa |
| load_shark4r_fields | Load SHARK4R fields from GitHub |
| load_shark4r_stats | Load SHARK4R statistics from GitHub |
| lookup_xy | Lookup spatial information for geographic points |
| 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 |
| match_dyntaxa_taxa | Match Dyntaxa taxon names |
| match_station | Match station names against SMHI station list |
| match_worms_taxa | Retrieve WoRMS records by taxonomic names with retry logic |
| parse_scientific_names | Parse scientific names into genus and species components. |
| plot_map_leaflet | Create an interactive Leaflet map of sampling stations |
| positions_are_near_land | Determine if positions are near land |
| read_ptbx | Read a Plankton Toolbox export file |
| 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) |
| run_qc_app | Launch the SHARK4R Bio-QC Tool |
| scatterplot | Scatterplot with optional horizontal threshold lines |
| translate_shark_datatype | Translate SHARK4R datatype names |
| update_dyntaxa_taxonomy | Update SHARK taxonomy records using Dyntaxa |
| which_basin | Determine if points are in a specified sea basin |