Retrieve SHARK Table Data

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).

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.

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.

Examples

if (FALSE) { # \dontrun{
  # 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)
} # }

Usage

Arguments

Value

Details

See also

Examples