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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 whether a movement line passes by (or through) the point. If a point is farther than radius from a great circle line between two cells centers then it is not between them.

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.

weighted

If FALSE use the original and quicker version of bmtr that sums all the marginal probability for transitions that pass within a fixed distance of the point. If TRUE assign a weight to the point and transition combo that then is multiplied by the marginal probability before summing. This argument is experimental but the default value is identical to the old version. The argument name and behavior when set to TRUE may change.

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.