getLocalObjects: Local Objects Identification

In nimbleSCR: Spatial Capture-Recapture (SCR) Methods Using 'nimble'

Local Objects Identification

Description

R utility function to identify all objects (e.g. traps) within a given radius dmax of each cell in a habitat mask. Used in the implementation of the local evaluation approach in SCR models (dbinomLocal_normal;dpoisLocal_normal). The distance to the activity center and the detection probability are then calculated for local objects only (i.e. the detection probability is assumed to be 0 for all other objects as they are far enough from the activity center).

Usage

getLocalObjects(habitatMask, coords, dmax, resizeFactor = 1, plot.check = TRUE)

Arguments

habitatMask	a binary matrix object indicating which cells are considered as suitable habitat.
coords	A matrix giving the x- and y-coordinate of each object (i.e. trap). x- and y- coordinates should be scaled to the habitat (scaleCoordsToHabitatGrid).
dmax	The maximal radius from a habitat cell center within which detection probability is evaluated locally for each trap.
resizeFactor	An aggregation factor to reduce the number of habitat cells to retrieve local objects for. Defaults to 1; no aggregation.
plot.check	A visualization option (if TRUE); displays which objects are considered "local objects" for a randomly chosen habitat cell.

Details

The getLocalObjects function is used in advance of model building.

Value

This function returns a list of objects:

• localIndices: a matrix with number of rows equal to the reduced number of habitat grid cells (following aggregation). Each row gives the id numbers of the local objects associated with this grid cell.

• habitatGrid: a matrix of habitat grid cells ID corresponding to the row indices in localIndices.

• numLocalIndices: a vector of the number of local objects for each habitat grid cell in habitatGrid.

• numLocalIndicesMax: the maximum number of local objects for any habitat grid cell ; corresponds to the number of columns in habitatGrid.

• resizeFactor: the aggregation factor used to reduce the number of habitat grid cells.

Author(s)

Cyril Milleret and Pierre Dupont

Examples

colNum <- sample(20:100,1)
rowNum <- sample(20:100,1)
coords <- expand.grid(list(x = seq(0.5, colNum, 1),
                               y = seq(0.5, rowNum, 1)))

habitatMask <- matrix(rbinom(colNum*rowNum, 1, 0.8), ncol = colNum, nrow = rowNum)

localObject.list <- getLocalObjects(habitatMask, coords,  dmax = 7,resizeFactor = 1)

nimbleSCR documentation built on Dec. 1, 2022, 1:17 a.m.