calculateDensity: NIMBLE function to calculate the density of individuals alive...

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

NIMBLE function to calculate the density of individuals alive in each habitat cell.

Description

calculateDensity is a NIMBLE function to calculate number of individual activity centers (s) in each habitat cell.

Usage

calculateDensity(s, habitatGrid, indicator, numWindows, nIndividuals)

Arguments

s	Matrix of x- and y-coordinates of individual AC locations.
habitatGrid	Matrix of habitat window indices. Cell values should correspond to the order of habitat windows in spatial probabilities (e.g. prob1To2Hab as used in the function dcatState1Alive2Dead) or in lowerCoords and upperCoords as used in the dbernppAC function. #' @param indicator Vector of binary arguments specifying whether the individuals are considered alive (indicator = 1) or not (indicator = 0).
indicator	Vector of binary arguments specifying whether the individuals are considered alive (indicator = 1) or not (indicator = 0).
numWindows	Scalar Number of habitat windows.
nIndividuals	Scalar Number of individuals.

Author(s)

Cyril Milleret

Examples

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)  
logIntensities <- log(rep(1,4))
logSumIntensity <- log(sum(c(1:4))) 
habitatGrid <- matrix(c(1:4), nrow = 2, byrow = TRUE)
numGridRows <- nrow(habitatGrid)
numGridCols <- ncol(habitatGrid)

s <- matrix(NA,nrow=10,ncol=2)
for(i in 1:10){
  s[i,] <- rbernppAC(n=1, lowerCoords, upperCoords, logIntensities, logSumIntensity, 
                     habitatGrid, numGridRows, numGridCols)
}

calculateDensity(s = s,
                 habitatGrid = habitatGrid,
                 indicator = rep(1, 10),
                 numWindows = prod(dim(habitatGrid)),
                 nIndividuals = 10
)

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