export_wastd_turtledata: Export all WAStD turtledata to CSV and GeoJSON files

In parksandwildlife/wastdr: WA Sea Turtle Database 'WAStD' API Wrapper

Export all WAStD turtledata to CSV and GeoJSON files

Description

Export all WAStD turtledata to CSV and GeoJSON files

Usage

export_wastd_turtledata(
  x,
  outdir = here::here(),
  filename = "export",
  zip = FALSE
)

Arguments

x	An object of class wastd_data as returned by download_wastd_turtledata. This data can optionally be filtered to an area_name (WAStD Area of type Locality).
outdir	The destination to write exported data to, default: here::here().
filename	The filename for the ZIP archive, default: export.
zip	Whether to archive the files as ZIP or keep them separate. Default: FALSE (keep separate files).

Value

A set of files in the folder outdir. GeoJSON files can be opened in any GIS, such as Quantum GIS or ESRI ArcGIS. CSV files can be opened in any spreadsheet program, such as MS Excel or LibreOffice Calc.

• areas.geojson WAStD Areas, or Localities.

  • Typically one locality per monitoring program.

• sites.geojson WAStD Sites.

  • Each Survey and Encounter can be linked to one Site.

• surveys.csv Surveys.

  • Each row is one Survey.

  • Training and duplicate Surveys are distinguished from production (real) Surveys by the column production (TRUE or FALSE).

• animals.csv AnimalEncounters.

  • This includes encounters with animals during turtle tagging, as well as strandings and rescues. Mind that stranded turtles can be tagged, but are not always encountered during dedicated surveys.

  • Survey details are repeated for convenience.

  • One record can have several additional observations, which are included as separate CSVs.

• turtle_tags.csv Tags recorded during an AnimalEncounter.

  • Each record concerns exactly one Tag.

  • One Animal can carry multiple Tags.

  • Details of the overarching AnimalEncounter are repeated for convenience.

• turtle_dmg.csv Damages or distinguishing features observed during an AnimalEncounter.

  • Each record concerns exactly one Damage.

  • One Animal can show multiple Damages or distinguishing features.

  • Details of the overarching AnimalEncounter are repeated for convenience.

• turtle_morph.csv Morphological measurements taken during an AnimalEncounter.

  • Each record concerns exactly one set of measurements.

  • One Animal could have multiple sets of measurements, although normally only one set of morphological measurements is taken.

  • Details of the overarching AnimalEncounter are repeated for convenience.

• tracks.csv TurtleNestEncounters, which include turtle tracks without nests ("false crawls"), nests with tracks ("successful crawls"), and any shade of doubt or negligent data capture in between.

  • One record is exactly one Track or Nest.

  • Survey details are repeated for convenience.

  • One record can have several additional observations, which are included as separate CSVs.

• nest_dist.csv TurtleNestDisturbanceObservations are recorded either linked to a nest (predated or damaged turtle nest), or standalone as general disturbance or predator presence.

  • Disturbed or predated nests are distinguished from general disturbance or predator presence through the column encounter_type ("nest" or "other").

  • Details of the overarching TurtleNestEncounter are repeated for convenience.

• nest_tags.csv NestTagObservations. A stick with an ID scribbled on it stuck in the sand next to a nest.

  • Not to be confused with data loggers, which also carry an ID and are associated with a turtle nest for a while.

  • Details of the overarching TurtleNestEncounter are repeated for convenience.

• nest_excavations.csv Excavations of a turtle nest, resulting in a count of eggs and leftovers grouped into categories, plus egg chamber details.

  • Details of the overarching TurtleNestEncounter are repeated for convenience.

• hatchling_morph.csv Morphometric measurements of a single turtle hatchling.

  • There can be several per nest.

  • Details of the overarching TurtleNestEncounter are repeated for convenience.

• nest_fans.csv Measurements of turtle hatchling emergence track fans.

  • Multiple measurements of fan angles per nest are possible, but not expected.

  • Details of the overarching TurtleNestEncounter are repeated for convenience.

• nest_fan_outliers.csv Individual hatchling tracks outside of the main fan of hatchling tracks.

  • There can be several per nest.

  • Details of the overarching TurtleNestEncounter are repeated for convenience.

• nest_lightsources.csv Individual known lightsources during hatching.

  • There can be several per nest.

  • Details of the overarching TurtleNestEncounter are repeated for convenience.

• nest_loggers.csv Deployed or re-sighted data loggers in a turtle nest.

  • There can be several per nest.

  • Details of the overarching TurtleNestEncounter are repeated for convenience.

• line_transects.csv Tallies turtle tracks along a transect, recorded during one LineTransectEncounter.

  • One record per transect.

  • Latitude and Longitude are extracted from the first waypoint of the line transect.

  • A transect can be crossed by many individual tracks.

• line_transects.geojson Data from line_transects.csv as GeoJSON. Currently excluded.

• track_tally.csv Tally of tracks by type and species crossing a transect.

  • There can be many tallies per transect.

  • Details of the overarching LineTransectEncounter are repeated for convenience.

• disturbance_tally.csv Tally of general disturbances or predator presence encountered during one LineTransectEncounter.

  • There can be several per transect.

  • Details of the overarching LineTransectEncounter are repeated for convenience.

• wastd_data.rds The given wastd_data object saved to file as .rds, ready to be loaded into R with readRDS.

See Also

Other api: build_auth(), download_minimal_wastd_turtledata(), download_wastd_sites(), download_wastd_turtledata(), download_wastd_users(), filter_wastd_turtledata_area(), filter_wastd_turtledata_seasons(), filter_wastd_turtledata(), handle_http_status(), wastd_GET(), wastd_POST(), wastd_bulk_post(), wastd_chunk_post(), wastd_create_update_skip(), wastd_parse(), wastd_post_one()

Examples

## Not run: 
data("wastd_data", package = "wastdr")
an <- "Ningaloo"
au <- urlize(an)
wastd_data %>%
  filter_wastd_turtledata(area_name = an) %>%
  export_wastd_turtledata(outdir = here::here(au), filename = au)

## End(Not run)

parksandwildlife/wastdr documentation built on Nov. 17, 2022, 4:52 p.m.