migration_matrix: Create Migration Matrix from a Migration object and a...

In petrelharp/landsim: Simulate Populations on Landscapes

Description

This returns the (sparse) Matrix giving the pseudo-adjacency matrix from and to for specified cells in the given Raster, with weights.

Usage

migration_matrix(population, accessible, migration = list(sigma = 1, normalize
  = 1), kern = migration$kern, sigma = migration$sigma,
  radius = migration$radius, normalize = migration$normalize,
  from = which(accessible), to = from, discretize = migration$discretize,
  disc.fact = 10, n.chunks = 1)

Arguments

population	Population object or Raster*.
accessible	Logical vector indicating which cells in 'habitat' that migrants will attempt to go to.
migration	Migration object; is overridden by other parameters below.
kern	Weighting kernel applied to distances.
sigma	Distance scaling for kernel.
radius	Maximum distance away to truncate the kernel.
normalize	If not NULL, migration weights to accessible locations are set to sum to this (see details).
from	The indices of the cells corresponding to rows in the output matrix. [default: non-NA cells]
to	The indices of the cells corresponding to columns in the output matrix. [default: same as from]
discretize	Whether or not to "discretize" the kernel first using the discretize_kernel function.
disc.fact	The discretization factor, if used (see discretize_kernel).
n.chunks	Number of chunks to compute the matrix in (can help with memory usage).

Value

A sparse Matrix M, where for each pair of cells i in from and i in to, the value M[i,j] is kern( d[i,j]/sigma ) or, if kern="gaussian", exp( - d[i,j]^2/sigma^2 ) / ( 2 pi sigma^2 ) * (area of a cell) where d[i,j] is the distance from from[i] to to[j], if this is greater than min.prob, and is 0 otherwise.

Summary of how to encode different types of boundary: set absorbing boundary elements to accessible, but do not include them in from (and to). Mark reflecting (non-)boundaries as not accessible. External boundaries will be reflecting, so if they should be absorbing, you need to extend the raster and set values appropriately.

Migration is possible to each accessible cell in the Raster*. If normalize is not NULL, then for each cell, the set of migration weights to each other accessible cell within distance radius is normalized to sum to normalize. The resulting matrix may not have rows summing to normalize, however, if from is a subset of the accessible ones.

If not normalized, the kernel is multiplied by the area of the cell (taken to be approximately constant).

The usual way to use this is to call migration_matrix(pop,mig), where pop is a population object, which contains both the Raster and the vector of which locations are accessible; and mig is a migration object containing the kernel, migration radius, etcetera.

Alternatively, population can be a RasterLayer, in which case by default all non-NA cells are accessible.

Inaccessible cells included in to, have zero migration outwards. Inaccessible cells included in from behave as usual.

petrelharp/landsim documentation built on May 25, 2019, 2:53 a.m.