R: Accessing and Validating Marine Environmental Data from 'SHARK' and Related Databases

# Accessing and Validating Marine Environmental Data from 'SHARK' and Related Databases

## Documentation for package ‘SHARK4R’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add_worms_taxonomy | Add WoRMS taxonomy hierarchy to AphiaIDs or scientific names
assign_phytoplankton_group | Assign phytoplankton group to scientific names
calc_zooplankton_biomass | Calculate zooplankton biomass from dry weight and abundance
calc_zooplankton_dry_weight | Calculate zooplankton dry weight from mean length
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
create_pie_map | Pie chart map with displacement and leader lines
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 Microalgae
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_image_labeling_links | Retrieve image labeling media links from Nordic Microalgae
get_nua_image_labeling_metadata | Retrieve image labeling metadata from Nordic Microalgae
get_nua_media_links | Retrieve and extract media URLs from Nordic Microalgae
get_nua_media_metadata | Retrieve media metadata 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