get_detection_containers: Define detection containers around receivers

In edwardlavender/flapper: Routines for the Analysis of Passive Acoustic Telemetry Data

Define detection containers around receivers

Description

This function defines the areas surveyed by receivers (termed ‘detection containers’) as a spatial object, based on an estimate of the detection range (m) and any barriers to detection. To implement the function, receiver locations must be supplied as a SpatialPoints or SpatialPointsDataFrame object with the Universe Transverse Mercator coordinate reference system. The function defines a spatial buffer around each receiver according to the estimated detection range, cuts out any barriers to detection, such as the coastline, and returns a SpatialPolygons object that defines the combined detection container across all receivers or receiver-specific detection containers.

Usage

get_detection_containers(
  xy,
  detection_range = 425,
  resolution = 1000,
  boundaries = NULL,
  coastline = NULL,
  plot = TRUE,
  ...
)

Arguments

xy	A SpatialPoints-class or SpatialPointsDataFrame-class object that defines receiver locations. The coordinate reference system should be the Universe Transverse Mercator coordinate reference system.
detection_range	A number that defines the detection range (m) of receivers.
resolution	A number that defines the number of linear segments used to approximate the detection container (see the quadsegs argument in gBuffer).
boundaries	An extent object (on an object from which this can be extracted) that defines the boundaries of the study area.
coastline	(optional) A SpatialPolygonsDataFrame-class object that defines barriers (such as the coastline) that block receivers from surveying areas within their detection range.
plot	A logical input that defines whether or not to plot receivers, their containers, and the buffer (if specified).
...	Additional arguments passed to gBuffer, such as byid.

Value

The function returns a SpatialPolygons-class object of the detection containers around receivers that represents the area they survey under the assumption of a constant detection range, accounting for any barriers to detection. By default, this will contain a single feature, which is suitable for the calculation of the total area surveyed by receivers (see get_detection_area_sum) because it accounts for the overlap in the detection ranges of receivers. However, if byid = TRUE is passed via ... to gBuffer, the returned object will have a feature for each pair of coordinates in xy (i.e., receiver). This is less appropriate for calculating the area surveyed by receivers, since areas surveyed by multiple receivers will be over-counted, but it is suitable when the containers for particular receivers are required (e.g., to extract environmental conditions within a specific receiver's detection range) (see get_detection_containers_envir).

Author(s)

Edward Lavender

Examples

#### Define receiver locations as a SpatialPoints object with a UTM CRS
proj_wgs84 <- sp::CRS(SRS_string = "EPSG:4326")
proj_utm <- sp::CRS(SRS_string = "EPSG:32629")
xy <- sp::SpatialPoints(
  dat_moorings[, c("receiver_long", "receiver_lat")],
  proj_wgs84
)
xy <- sp::spTransform(xy, proj_utm)
xy@data <- as.data.frame(xy)

#### Example (1): Get the simplest containers around receivers
get_detection_containers(xy)

#### Example (2): Account for barriers in the study area
get_detection_containers(xy, coastline = dat_coast)

#### Example (3): Adjust the detection range
get_detection_containers(xy, detection_range = 400, coastline = dat_coast)
get_detection_containers(xy, detection_range = 500, coastline = dat_coast)

#### Example (4): Suppress the plot
get_detection_containers(xy, coastline = dat_coast, plot = FALSE)

#### Example (5): Output characteristics are controlled via byid
# A SpatialPolygons object with one feature is the implicit output
sp_1 <- get_detection_containers(xy, coastline = dat_coast, byid = FALSE)
sp_1
# A SpatialPolygons object with one feature for each element in xy
# ... can be returned via byid = TRUE
sp_2 <- get_detection_containers(xy, coastline = dat_coast, byid = TRUE)
sp_2
# The total area of the former will be smaller, since areas covered
# ... by multiple receivers are merged
rgeos::gArea(sp_1)
rgeos::gArea(sp_2)
# But it can be more convenient to use the latter format in some cases
# ... because it is easy to isolate specific containers:
raster::plot(dat_coast)
raster::plot(sp_1[1], add = TRUE, col = "red") # single feature
raster::plot(sp_2[1], add = TRUE, col = "blue") # isolate specific features

edwardlavender/flapper documentation built on Jan. 22, 2025, 2:44 p.m.