simulate_dispersal {dispeRse}R Documentation

Simulates first arrival times from one or more origins.

Description

The model uses density-dependent growth and emigration. The carrying capacity, growth rates and mobility are allowed to vary with the environment.

Usage

simulate_dispersal(
  environment,
  terrain,
  coords,
  years,
  r = 0.025,
  phi = 0.5,
  t = 30,
  dist = 50,
  accel = 3,
  gamma = 1,
  updates = NULL,
  verbose = TRUE
)

Arguments

environment

A Raster*. Environmental values that affect carrying capacity and growth rate. Typically given as a fraction (0-1) of the max K. If the environment will be updated during the experiment, this parameter must be a raster stack.

terrain

A Raster*. Cells with value 1 are barriers and cells with value 2 are corridors. If the terrain will be updated during the experiment, this parameter must be a raster stack.

coords

A DataFrame. Must contain columns x, y, and date with the coordinates and starting date (yr BP) of each origin. Coordinates must be in the same system as the environment and terrain layers.

years

Numeric. Number of years to run the model for.

r

Numeric. The annual growth rate as a decimal.

phi

Numeric. The emigration threshold as a fraction of carrying capacity.

t

Numeric. The duration, in years, of a generation (model time step).

dist

Numeric. The distance, in km, that migrants move over a generation.

accel

Numeric. The factor by which the usual distance is increased along corridors. E.g. if dist = 50 km and accel = 3, migrants can move up to 150 km along a corridor. Must range from 2 to 4.

gamma

Numeric. A power that controls the shape of the dependency between r and the environment.

updates

Numeric. Optional vector with the years at which the environment and terrain grids will be updated.

verbose

Boolean. If TRUE, write messages to the console.

Details

The simulation starts with n populated cells at coordinates and start times defined by the parameter coords and runs for a number of time. Each time step corresponds to a generation (defined by parameter t). Growth is applied to every populated cell using a logistic model and emigration to a neighboring cell is calculated from an asymptotic threshold model.

The carrying capacity (K) in the density-dependend growth and emigration models is determined by an environment raster, which normally represents a variable or combination of variables assumed to affect population density (e.g. net primary production, elevation) scaled to 0-1 range.

The dependence of the carrying capacity and growth rate on the environment is allowed to be controlled by a power gamma. By default, the dependence is linear (gamma = 1).

For emigration, a threshold phi is considered, expressed as a fraction of carrying capacity. Migrants are distributed among the available cells of the Moore neighborhood proportionally to the inverse of the distance squared.

Terrain can be represented by a raster specifying barriers (e.g. mountains), which block movement, and corridors (e.g. rivers), which accelerate movement. For the latter, an acceleration factor can be specified.

Value

A RasterLayer with simulated arrival times.

Examples

terr <- raster::stack(replicate(8, euro_terr))
sim <- simulate_dispersal(euro_npp, terr, ppnb, 5500, phi=0.33, updates=seq(10000,4000,-1000))

[Package dispeRse version 1.0 Index]