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Datasets: the MEFS project

Source: R/dats-mefs.R
datasets-mefs.Rd

These are sample datasets collated by the Movement Ecology of Flapper Skate (MEFS) project (Lavender, 2022). The flapper skate (Dipturus intermedius) is a Critically Endangered benthic elasmobranch. As part of the MEFS project, flapper skate were tagged with acoustic transmitters and archival (data storage) tags off the west coast of Scotland in 2016–17. Acoustic transmissions were recorded at an array of passive acoustic telemetry receivers. Concurrent depth time series were recorded by archival tags and recovered from recaptured individuals. For full details, see the references below. The datasets are defined within patter to illustrate package functions using real-world datasets.

Usage

dat_moorings

dat_detections

dat_archival

dat_gebco(.return = c("SpatRaster", "character"))

dat_coast(.return = c("SpatVector", "character"))

dat_mpa(.return = c("SpatVector", "character"))

Format

An object of class data.table (inherits from data.frame) with 40 rows and 8 columns.

An object of class data.table (inherits from data.frame) with 39242 rows and 3 columns.

An object of class data.table (inherits from data.frame) with 75000 rows and 3 columns.

Source

Biologging and biotelemetry data were collected by, and belong to, Marine Scotland Science and NatureScot. Data were processed by Lavender (2022). If you wish to use these data, please contact Marine Scotland Science and NatureScot for further information.

Bathymetry data were sourced from GEBCO Compilation Group (2019) GEBCO 2019 Grid. https://www.doi.org/10.5285/836f016a-33be-6ddc-e053-6c86abc0788e

Coastline data were sourced from flapper::dat_coast.

MPA boundary data were assembled by E. Lavender.

Arguments

.return

A character that defines the object returned by dat_gebco(), dat_coast() or dat_mpa():

  • SpatRaster returns a terra::SpatRaster;

  • SpatVector returns a terra::SpatVector;

  • character returns a file path to the raster. This is the only supported option on Linux if JULIA_SESSION = "TRUE";

Moorings

dat_moorings defines passive acoustic telemetry receiver locations and associated information. This includes the following columns:

  • receiver_id—an integer vector that defines unique receiver deployments;

  • receiver_start, receiver_end—Date vectors that define receiver deployment start and end dates;

  • receiver_x, receiver_y—numeric vectors that define receiver coordinates (in UTM 29N);

  • receiver_alpha, receiver_beta, receiver_gamma—a numeric vectors that define detection probability parameters;

Data are arranged by receiver_id.

Detections

dat_detections contains sample detection time series. This includes the following columns:

  • individual_id—an integer vector that identifies individuals;

  • timestamp—a POSIXct vector that defines the time of each observation;

  • receiver_id—the receiver ID (see dat_moorings);

Data are arranged by individual_id, timestamp and then receiver_id.

Archival

dat_archival contains sample depth time series. Observations were sampled every 2 minutes. The data includes the following columns:

  • individual_id—an integer vector that identifies individuals (as in dat_detections);

  • timestamp—a POSIXct vector that defines the time of each observation;

  • depth—a numeric vector that defines the depth (m) of the individual at each time step;

Data are arranged by individual_id and then timestamp.

Bathymetry

dat_gebco() returns a bathymetry (m) dataset for the west coast of Scotland where MEFS data were collected. This dataset is a terra::SpatRaster with the following properties:

  • dimensions—264, 190, 1 (nrow, ncol, nlyr);

  • resolution—100, 100 (x, y);

  • extent—695492.1, 714492.1, 6246657, 6273057 (xmin, xmax, ymin, ymax);

  • coord. ref.—WGS 84 / UTM zone 29N (EPSG:32629);

Coastline

dat_coast() returns a terra::SpatVector of coastline for the same region.

Marine Protected Area

dat_mpa() returns a terra::SpatVector of the boundaries of the Loch Sunart to the Sound of Jura Marine Protected Area (MPA) with the following columns:

  • id—A character label for each polygon;

  • open—A character that defines whether or not each id is open or closed to fishing;

  • col—A character that defines a colour (for visualising);

References

Data collection and processing are described in Lavender (2022). Modelling the movements of flapper skate (Dipturus intermedius) in relation to a Scottish Marine Protected Area. University of St Andrews. https://www.doi.org/10.17630/sta/201

For further information on the MEFS project, see: