get_shark_table: Retrieve SHARK Table Data

In sharksmhi/SHARK4R: Retrieving, Analyzing, and Validating Marine Data from SHARK and Nordic Microalgae

Retrieve SHARK Table Data

Description

This function has been deprecated due to inefficiency in handling large datasets. Users are encouraged to use get_shark_data for such cases. However, the get_shark_table function remains effective for retrieving smaller datasets (< 10^5 rows) from the SHARK database hosted by SMHI. Its functionality is similar to the table view available at https://shark.smhi.se/. For larger requests, switch to get_shark_data, and to explore available filter options, see get_shark_options.

Usage

get_shark_table(
  tableView = "sharkweb_overview",
  limit = 0,
  headerLang = "internal_key",
  fromYear = 2019,
  toYear = 2020,
  months = c(),
  dataTypes = c(),
  parameters = c(),
  orderers = c(),
  qualityFlags = c(),
  deliverers = c(),
  projects = c(),
  datasets = c(),
  minSamplingDepth = "",
  maxSamplingDepth = "",
  checkStatus = "",
  redListedCategory = c(),
  taxonName = c(),
  stationName = c(),
  vattenDistrikt = c(),
  seaBasins = c(),
  counties = c(),
  municipalities = c(),
  waterCategories = c(),
  typOmraden = c(),
  helcomOspar = c(),
  seaAreas = c(),
  prod = TRUE,
  verbose = TRUE
)

Arguments

tableView	Character. Specifies the view of the table to retrieve. Options include: "sharkweb_overview": Overview table "sharkweb_all": All available columns "sharkdata_bacterioplankton": Bacterioplankton table "sharkdata_chlorophyll": Chlorophyll table "sharkdata_epibenthos": Epibenthos table "sharkdata_greyseal": Greyseal table "sharkdata_harbourporpoise": Harbour porpoise table ⁠"sharkdata_harbourseal⁠: Harbour seal table "sharkdata_jellyfish": Jellyfish table "sharkdata_physicalchemical": Physical chemical table "sharkdata_physicalchemical_columns": Physical chemical table: column view "sharkdata_phytoplankton": Phytoplankton table "sharkdata_picoplankton": Picoplankton table "sharkdata_planktonbarcoding": Plankton barcoding table "sharkdata_primaryproduction": Primary production table "sharkdata_ringedseal": Ringed seal table "sharkdata_sealpathology": Seal pathology table "sharkdata_sedimentation": Sedimentation table "sharkdata_zoobenthos": Zoobenthos table "sharkdata_zooplankton": Zooplankton table "report_sum_year_param": Report sum per year and parameter "report_sum_year_param_taxon": Report sum per year, parameter and taxon "report_sampling_per_station": Report sampling per station "report_obs_taxon": Report observed taxa "report_stations": Report stations "report_taxon": Report taxa Default is "sharkweb_overview".
limit	Integer. Maximum number of records to retrieve per request. Default is 0 (all records). Maximum 10^5.
headerLang	Character. Language option for column headers. Possible values: "sv": Swedish "en": English "short": Shortened version "internal_key": Internal key (default)
fromYear	Integer. The starting year for the data to retrieve. Default is 2019.
toYear	Integer. The ending year for the data to retrieve. Default is 2020.
months	Integer vector. The months to retrieve data for, e.g., c(4, 5, 6) for April to June.
dataTypes	Character vector. Specifies data types to filter, such as "Chlorophyll" or "Epibenthos".
parameters	Character vector. Optional vector of parameters to filter results, such as "Chlorophyll-a".
orderers	Character vector. Optional vector of orderers to filter data by specific individuals or organizations.
qualityFlags	Character vector. Optional vector of quality flags to filter data.
deliverers	Character vector. Optional vector of deliverers to filter data by data providers.
projects	Character vector. Optional vector of projects to filter data by specific research or monitoring projects.
datasets	Character vector. Optional vector of datasets to filter data by specific dataset names.
minSamplingDepth	Numeric. Optional minimum depth (in meters) for sampling data to filter results.
maxSamplingDepth	Numeric. Optional maximum depth (in meters) for sampling data to filter results.
checkStatus	Character string. Optional status check to filter results.
redListedCategory	Character vector. Optional vector of red-listed taxa for conservation filtering.
taxonName	Character vector. Optional vector of taxa names for filtering specific species or taxa.
stationName	Character vector. Optional vector of station names to retrieve data from specific stations.
vattenDistrikt	Character vector. Optional vector of water district names to filter data by Swedish water districts.
seaBasins	Character vector. Optional vector of sea basin names to filter data by different sea areas.
counties	Character vector. Optional vector of counties to filter data within specific administrative regions in Sweden.
municipalities	Character vector. Optional vector of municipalities to filter data within specific local administrative regions.
waterCategories	Character vector. Optional vector of water categories to filter from.
typOmraden	Character vector. Optional vector of type areas to filter data by specific areas.
helcomOspar	Character vector. Optional vector of HELCOM or OSPAR areas for regional filtering.
seaAreas	Character vector. Optional vector of sea area codes for filtering by specific sea areas
prod	Logical. Query against PROD or TEST (SMHI internal) server. Default is TRUE (PROD).

Details

This function constructs a JSON body with specified parameters and sends a POST request to the SHARK API. The API returns data in JSON format, which is then parsed into a data.frame. If rows have differing lengths, rbind.fill fills missing columns with NA.

Value

A data.frame containing the retrieved data, with column names based on the API's headers. Columns are filled with NA when rows have differing lengths.

See Also

get_shark_options

Examples

## Not run: 
  # Retrieve chlorophyll data for April to June from 2019 to 2020
  shark_data <- get_shark_table(fromYear = 2019, toYear = 2020,
                                months = c(4, 5, 6), dataTypes = c("Chlorophyll"))
  View(shark_data)

## End(Not run)

sharksmhi/SHARK4R documentation built on Jan. 9, 2025, 5:15 p.m.