View source: R/getLocalObjects.R
getLocalObjects | R Documentation |
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).
getLocalObjects(habitatMask, coords, dmax, resizeFactor = 1, plot.check = TRUE)
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 ( |
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. |
The getLocalObjects
function is used in advance of model building.
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.
Cyril Milleret and Pierre Dupont
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)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.