Man pages for sharksmhi/SHARK4R
Retrieving, Analyzing, and Validating Marine Data from SHARK and Nordic Microalgae
| add_hierarchy_column | Add Taxonomic Hierarchy Column to a Dataset |
| add_worms_taxonomy | Retrieve and Organize WoRMS Taxonomy for SHARK Aphia IDs |
| assign_phytoplankton_group | Assign Phytoplankton Group to Scientific Names |
| check_algaebase_api | Check AlgaeBase API Operational Status |
| check_bacterial_carbon | Uses data from national marine monitoring for the last 5... |
| check_bacterial_concentration | Uses data from national marine monitoring for the last 5... |
| check_bacterial_production | Uses data from national marine monitoring for the last 5... |
| check_Bacterioplankton | Check if the required and recommended datatype-specific SHARK... |
| check_Chlorophyll | Check if the required and recommended datatype-specific SHARK... |
| check_chlorophyll_conc | Uses data from national marine monitoring for the last 5... |
| check_code_proj | Check matches of reported project (PROJ) codes in SMHIs... |
| check_datatype | Check if the required and recommended global and... |
| check_deliv_Bacterioplankton | Check if the required and recommended global and... |
| check_deliv_Chlorophyll | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_Epibenthos | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_EpibenthosDropvideo | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_GreySeal | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_HarbourPorpoise | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_HarbourSeal | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_PhysicalChemical | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_Phytoplankton | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_Picoplankton | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_PrimaryProduction | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_RingedSeal | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_SealPathology | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_Sedimentation | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_Zoobenthos | Check if the required and recommended datatype-specific SHARK... |
| check_deliv_Zooplankton | Check if the required and recommended datatype-specific SHARK... |
| check_depth | Check which points have potentially invalid depths. |
| check_Epibenthos | Check if the required and recommended datatype-specific SHARK... |
| check_epibenthos_abundclass_logical | Check logical assumptions of data for specific variables and... |
| check_epibenthos_counted | Uses data from national marine monitoring for the last 5... |
| check_epibenthos_coverclass_logical | Check logical assumptions of data for specific variables and... |
| check_epibenthos_cover_logical | Check logical assumptions of data for specific variables and... |
| check_epibenthos_coverpercent_logical | Check logical assumptions of data for specific variables and... |
| check_EpibenthosDropvideo | Check if the required and recommended datatype-specific SHARK... |
| check_epibenthos_dryweight | Uses data from national marine monitoring for the last 5... |
| check_epibenthos_sedimentdepos_logical | Check logical assumptions of data for specific variables and... |
| check_epibenthos_specdistr_maxdepth | Uses data from national marine monitoring for the last 5... |
| check_epibenthos_specdistr_mindepth | Uses data from national marine monitoring for the last 5... |
| check_epibenthos_totcover_logical | Check logical assumptions of data for specific variables and... |
| check_GreySeal | Check if the required and recommended datatype-specific SHARK... |
| check_greyseal_counted | Uses data from national marine monitoring for the last 5... |
| check_HarbourPorpoise | Check if the required and recommended datatype-specific SHARK... |
| check_HarbourSeal | Check if the required and recommended datatype-specific SHARK... |
| check_harbourseal_counted | Uses data from national marine monitoring for the last 5... |
| check_harbporp_positivemin | Uses data from national marine monitoring for the last 5... |
| check_onland | Check which points are located on land. |
| check_PhysicalChemical | Check if the required and recommended datatype-specific SHARK... |
| check_Phytoplankton | Check if the required and recommended datatype-specific SHARK... |
| check_phytoplankton_abund | Uses data from national marine monitoring for the last 5... |
| check_phytoplankton_biovol | Uses data from national marine monitoring for the last 5... |
| check_phytoplankton_carbon | Uses data from national marine monitoring for the last 5... |
| check_Picoplankton | Check if the required and recommended datatype-specific SHARK... |
| check_picoplankton_abundance | Uses data from national marine monitoring for the last 5... |
| check_picoplankton_biovol | Uses data from national marine monitoring for the last 5... |
| check_picoplankton_carbon | Uses data from national marine monitoring for the last 5... |
| check_picoplankton_counted | Uses data from national marine monitoring for the last 5... |
| check_PrimaryProduction | Check if the required and recommended datatype-specific SHARK... |
| check_primaryproduction_carbonprod | Uses data from national marine monitoring for the last 5... |
| check_primaryproduction_carbonprod_hour | Uses data from national marine monitoring for the last 5... |
| check_primaryproduction_carbonprodlight | Uses data from national marine monitoring for the last 5... |
| check_RingedSeal | Check if the required and recommended datatype-specific SHARK... |
| check_ringedseal_calccounted | Uses data from national marine monitoring for the last 5... |
| check_SealPathology | Check if the required and recommended datatype-specific SHARK... |
| check_Sedimentation | Check if the required and recommended datatype-specific SHARK... |
| check_station_distance | Station distance check using SMHI station list "stations.txt"... |
| check_value_logical | Check logical assumptions of data for specific variables and... |
| check_zero_positions | Check logical assumptions of data for station positions |
| check_zero_value | Check logical assumptions of data for specific variables and... |
| check_Zoobenthos | Check if the required and recommended datatype-specific SHARK... |
| check_zoobenthos_abund | Uses data from national marine monitoring for the last 5... |
| check_zoobenthos_BQIm | Uses data from national marine monitoring for the last 5... |
| check_zoobenthos_BQIm_logical | Check logical assumptions of data for specific variables and... |
| check_zoobenthos_counted | Uses data from national marine monitoring for the last 5... |
| check_zoobenthos_wetweight | Uses data from national marine monitoring for the last 5... |
| check_zoobenthos_wetweight_logical | Check logical assumptions of data for specific variables and... |
| check_Zooplankton | Check if the required and recommended datatype-specific SHARK... |
| check_zooplankton_abund | Uses data from national marine monitoring for the last 5... |
| check_zooplankton_carbon | Uses data from national marine monitoring for the last 5... |
| check_zooplankton_counted | Uses data from national marine monitoring for the last 5... |
| check_zooplankton_length_mean | Uses data from national marine monitoring for the last 5... |
| check_zooplankton_length_median | Uses data from national marine monitoring for the last 5... |
| check_zooplankton_wetweight | Uses data from national marine monitoring for the last 5... |
| check_zooplankton_wetweight_area | Uses data from national marine monitoring for the last 5... |
| check_zooplankton_wetweight_volume | Uses data from national marine monitoring for the last 5... |
| construct_dyntaxa_missing_table | Construct Dyntaxa Taxonomy Table From Individual API |
| construct_dyntaxa_table | Construct Dyntaxa Taxonomy Table From API |
| defunct | Defunct functions |
| extract_algaebase_field | Extract specific field from AlgaeBase query result |
| fill_na_below_first_non_na | Function to fill NA values below the first non-NA value in a... |
| find_descendants | Find All Descendants of a Taxon |
| get_algaebase_genus | Search AlgaeBase for Information About a Genus of Algae |
| get_algaebase_species | Algaebase Species Search |
| get_all_parents | Get All Parent Taxa for a Set of Taxon IDs |
| get_dyntaxa_children_hierarchy | Get children hierarchies for specified taxon IDs from SLU... |
| get_dyntaxa_children_ids | Get children taxon IDs for specified taxon IDs from SLU... |
| 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... |
| get_dyntaxa_records | Get taxonomic information from SLU Artdatabanken API for... |
| get_hab_list | Download the Harmful Algal Blooms (HABs) Taxonomic List |
| get_hierarchy | Recursively Retrieve Parent Taxonomic Hierarchy |
| get_nua_external_links | Retrieve External Links or Facts for Taxa from Nordic... |
| 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_shark_data | Retrieve Data from SHARK API |
| get_shark_options | Retrieve Available Search Options from SHARK API |
| get_shark_table | Retrieve SHARK Table Data |
| get_shark_table_counts | Retrieve SHARK Data Table Row Counts |
| get_toxin_list | Retrieve Toxin Data from IOC-UNESCO Toxins Database |
| get_worms_records | Retrieve WoRMS Records |
| get_worms_records_name | Retrieve WoRMS Records by Taxonomic Names with Retry Logic |
| ifcb_is_near_land | Determine if Positions are Near Land |
| ifcb_which_basin | Determine if Points are in a Specified Sea Basin |
| lookup_xy | Lookup spatial data for a set of points. |
| match_algaebase | Search Algaebase for Taxonomic Information |
| match_dyntaxa | Taxon matching using Dyntaxa (https://www.dyntaxa.se/) |
| match_station | Station matching using SMHI station list "stations.txt" (the... |
| match_taxon_name | Match Dyntaxa taxon names via API |
| match_wormstaxa | Taxon matching using WoRMS (http://www.marinespecies.org/)... |
| nominal_station | Check if stations are reported as nominal position or not... |
| parse_scientific_names | Parse scientific names into genus and species components. |
| 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-... |
| SHARK4R-package | SHARK4R: Retrieving, Analyzing, and Validating Marine Data... |
| shark_read | Read tab delimited files downloaded from SHARK Uses... |
| shark_read_deliv | Read .xlsx files delivered to SHARK Uses readxl to read excel... |
| shark_read_deliv_xls | Read .xls files delivered to SHARK Uses readxl to read excel... |
| shark_read_zip | Read zip archive and unzip tab delimited files downloaded... |
| update_dyntaxa_taxonomy | Update taxonomy from SHARK via SLU Artdatabanken API... |
| update_worms_taxonomy | Retrieve and Organize WoRMS Taxonomy for SHARK Aphia IDs |
