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Calculate Bird Flow Migration Traffic Rate

Source: R/calc_bmtr.R
calc_flux.Rd

DEPRECATED FUNCTION. Please use calc_bmtr() instead.

Usage

calc_flux(...)

Arguments

...

Arguments passed on to calc_bmtr

bf

A BirdFlow model

points

A set of points to calculate movement through. If points is NULL they will default to the BirdFlow model cells that are either active or fall between two active cells. Otherwise a data frame with x and y columns containing point coordinates in crs(bf).

radius

The radius in meters around the points used to assess the detection rate for a movement at the point. With method = "binary", if a point is within radius of the great circle line between two cell centers then the movement is detected at that point. For the two continuous detection methods there is a probability distribution for the location of the bird as it passes by the point, and the radius defines the band over which that probability is integrated, giving the detection rate.

n_directions

The number of directional bins to use for recording movement direction. Must be either 1 indicating no direction information or an even number. This is a placeholder, currently only 1 is supported.

format

The format to return the results in one of:

"points"

Returns a list with bmtr a matrix or array of bmtr values, and points a data frame of either the input points or the default cell center derived points.

"dataframe"

Returns a "long" data frame with columns:

  • x and y coordinates of the points.

  • transition Transition code.

  • bmtr The bmtr at the point. See "Units" below .

  • date The date associated with the transition, will be at the midpoint between timesteps.

"SpatRaster"

Returns a terra::SpatRaster with layers for each transition.

method

The detection model used to determine how much of a transition's movement counts towards a point's BMTR:

"binary"

(default) Fast and deterministic. A movement line either does or does not pass within radius of the point, per is_between().

"continuous"

Assigns a continuous weight (0 to 1) based on the probability that a bird's actual path, modeled as spreading away from the straight line between two cells, passes within radius of the point. Uses planar (Euclidean) geometry in the model's native CRS, and is the recommended detection model when continuous weighting is desired.

"continuous-spherical"

The same continuous weighting as "continuous", but computed with great-circle (spherical) geometry instead. Much slower, and not recommended for routine use; kept to allow assessing the impact of switching from spherical to Euclidean geometry.

batch_size

controls the number of movement lines that are processed at a time. A smaller batch_size will conserve memory at a slight performance cost. The number of batches will be less than or equal to n_active(bf)^2 / batch_size.

check_radius

If TRUE an error will be thrown if the radius is not between the resolution and 1/4 the resolution of bf. Outside of that range the algorithm is likely to yield distorted results. 0.5 * mean(res(bf)) is the default, and recommended radius.

Value

See format argument.