generate_nsf: Generate neighbour selection function

In mstrimas/metacapa: Metapopulation Capacity-based Conservation Prioritization

Description

Optimization by simulated annealing requires a function to select a neighbouring state to test given the current state. This function generates such a neighbour selection function. The resulting function will swap the status of a single planning unit.

Usage

generate_nsf(pu, buffer, locked, recalculate = 1L)

Arguments

pu	raster::RasterStack, sp::SpatialPolygonsDataFrame, or sf::sf object; planning units.
buffer	numeric; a buffer around the perimeter of the currently selected planning units in the units of the projection. Any planning units within this buffer will be considered for switching when generating a neighbouring state.
locked	name of a binary column (for vector data) or layer (for raster data) that specified planning units that are locked in or out and should be left unchanged. Alternatively, a integer vector of planning unit numbers may be supplied specifying units to leave unchanged.
recalculate	integer; frequency at which the set of planning units to consider for switching should be recalculated, e.g. a value of 100 would result in recalculating every 100 calls to the returned function. This process of recalculating can be computationally intensive for large sets of planning units, so choosing a larger value for recalculate will speed up processing time.

Details

In an attempt to more intelligently select a planning unit to switch, only those planning units meeting the following criteria will be considered:

• Units touching the boundary of the existing reserve network, whether inside or outside.

• Units within a defined distance, buffer, of the boundary of the existing reserve network.

This ensures that units in the interior of an existing reserve or far from an existing reserve are not changed.

Value

A function to choose a neighbouring state given a vector of binary decision variables. To return the list of planning units under consideration for switching use pu_list = TRUE.

Examples

# generate data
r <- raster::raster(nrows = 10, ncols = 10, crs = "+proj=aea", vals = 0)
# lock some units to be unchanged
names(r) <- "locked_out"
r[sample(1:100, 10)] <- 1
pus <- raster::rasterToPolygons(r)
selected <- sample(c(FALSE, TRUE), 100, replace = TRUE, prob = c(0.9, 0.1))

# generate neighbour selection function
neighbour <- generate_nsf(pus, buffer = 20, locked = "locked_out")

# neighbouring solution
neighbour(selected)
neighbour(selected, pu_list = TRUE)

mstrimas/metacapa documentation built on Dec. 3, 2019, 3:16 p.m.