nimbleSCR (version 0.2.1)

dbernppACmovement_exp: Bernoulli point process for activity center movement (exponential kernel)

Description

Density and random generation functions of the Bernoulli point process for activity center movement between occasions based on a bivariate exponential distribution.

Usage

dbernppACmovement_exp(
  x,
  lowerCoords,
  upperCoords,
  s,
  lambda = -999,
  rate,
  baseIntensities,
  habitatGrid,
  numGridRows,
  numGridCols,
  numWindows,
  log = 0
)
rbernppACmovement_exp(
  n,
  lowerCoords,
  upperCoords,
  s,
  lambda = -999,
  rate,
  baseIntensities,
  habitatGrid,
  numGridRows,
  numGridCols,
  numWindows
)

Value

dbernppACmovement_exp gives the (log) probability density of the observation vector x. rbernppACmovement_exp gives coordinates of a randomly generated spatial point.

Arguments

x

Vector of x- and y-coordinates of a single spatial point (typically AC location at time t+1) scaled to the habitat (see (scaleCoordsToHabitatGrid).

lowerCoords, upperCoords

Matrices of lower and upper x- and y-coordinates of all habitat windows. One row for each window. Each window should be of size 1x1 (after rescaling if necessary).

s

Vector of x- and y-coordinates of the isotropic multivariate exponential distribution mean (AC location at time t).

lambda

Rate parameter of the isotropic bivariate exponential distribution. Soon deprecated, use argument "rate" instead.

rate

Rate parameter of the isotropic multivariate exponential distribution.

baseIntensities

Vector of baseline habitat intensities for all habitat windows.

habitatGrid

Matrix of habitat window indices. Cell values should correspond to the order of habitat windows in lowerCoords and upperCoords. When the habitat grid only consists of a single row or column of windows, an additional row or column of dummy indices has to be added because the nimble model code requires a matrix.

numGridRows, numGridCols

Numbers of rows and columns of the habitat grid.

numWindows

Number of habitat windows. This value (positive integer) can be used to truncate lowerCoords and upperCoords so that extra rows beyond numWindows are ignored.

log

Logical argument, specifying whether to return the log-probability of the distribution.

n

Integer specifying the number of realisations to generate. Only n = 1 is supported.

Author

Wei Zhang and Cyril Milleret

Details

The dbernppACmovement_exp distribution is a NIMBLE custom distribution which can be used to model and simulate movement of activity centers between consecutive occasions in open population models. The distribution assumes that the new individual activity center location (x) follows an isotropic exponential normal centered on the previous activity center (s) with rate (lambda).

References

W. Zhang, J. D. Chipperfield, J. B. Illian, P. Dupont, C. Milleret, P. de Valpine and R. Bischof. 2020. A hierarchical point process model for spatial capture-recapture data. bioRxiv. DOI 10.1101/2020.10.06.325035

Examples

# Use the distribution in R
lowerCoords <- matrix(c(0, 0, 1, 0, 0, 1, 1, 1), nrow = 4, byrow = TRUE)
upperCoords <- matrix(c(1, 1, 2, 1, 1, 2, 2, 2), nrow = 4, byrow = TRUE)  
s <- c(1, 1) # Currrent activity center location
rate <- 0.1
baseIntensities <- c(1:4)
habitatGrid <- matrix(c(1:4), nrow = 2, byrow = TRUE)
numRows <- nrow(habitatGrid)
numCols <- ncol(habitatGrid)
numWindows <- 4
# The log probability density of moving from (1,1) to (1.2, 0.8) 
dbernppACmovement_exp(x = c(1.2, 0.8),
lowerCoords = lowerCoords,
upperCoords = upperCoords,
s = s,
rate = rate,
baseIntensities = baseIntensities, 
habitatGrid = habitatGrid,
numGridRows = numRows,
numGridCols = numCols,
numWindows = numWindows,
log = TRUE)