Skip to contents

Biological data sources

Source: R/sources_biological.R
sources_biological.Rd

Data sources providing selected Southern Ocean biological data sets. Please note that this is not intended to be a comprehensive collection of such data. Users are referred to the SCAR Standing Committee on Antarctic Data Management (https://www.scar.org/data-products/scadm/) and in particular the Antarctic Master Directory metadata catalogue (http://gcmd.nasa.gov/portals/amd/).

Usage

sources_biological(name, formats, time_resolutions, ...)

Arguments

name

character vector: only return data sources with name or id matching these values

formats

character: for some sources, the format can be specified. See the list of sources above for details

time_resolutions

character: for some sources, the time resolution can be specified. See the list of sources above for details

...

: additional source-specific parameters. See the list of sources above for details

Value

a tibble with columns as specified by bb_source

Details

  • "Southern Ocean Continuous Plankton Recorder": zooplankton species, numbers and abundance data are recorded on a continuous basis while vessels are in transit

  • "SEAPODYM Zooplankton & Micronekton weekly potential and biomass distribution": outputs of the SEAPODYM Low and Mid-Trophic Levels (LMTL) model, which simulates the spatial and temporal dynamics of six micronekton and one zooplankton functional groups between the sea surface and ~1000m depth

  • "SCAR RAATD model outputs": Single-species habitat importance maps for 17 species of Antarctic and subantarctic seabirds, marine mammals, and penguins

  • "SCAR RAATD data filtered": Tracking data from 17 species of Antarctic and subantarctic seabirds, marine mammals, and penguins. This data set is the 'filtered' version of the data files

  • "SCAR RAATD data standardised": Tracking data from 17 species of Antarctic and subantarctic seabirds, marine mammals, and penguins. This data set is the 'standardized' version of the data files

  • "Myctobase": A circumpolar database of Southern Ocean mesopelagic fish surveys, including occurrence and abundance information, as well as trait-based information of individuals including standard length, weight and life stage

The returned tibble contains more information about each source.

References

See the doc_url and citation field in each row of the returned tibble for references associated with these particular data sources

See also

sources_altimetry, sources_meteorological, sources_oceanographic, sources_reanalysis, sources_sdm, sources_seaice, sources_sst, sources_topography

Examples

## our local directory to store the data
my_data_dir <- tempdir()
cf <- bb_config(my_data_dir)

## our data source to download
src <- sources("Myctobase")

## add to our config
cf <- bb_add(cf, src)

## and sync it
if (interactive()) {
  status <- bb_sync(cf)
}

## or equivalently
if (interactive()) {
  status <- bb_get(sources("Myctobase"), local_file_root = my_data_dir)
}