getHomeRangeArea: Computation of home range radius and area

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

Computation of home range radius and area

Description

getHomeRangeArea returns approximates estimates of home range radius and area for a given set of parameters with respect to a specified detection function using bisection algorithm. The following circular detection functions are available to use in nimbleSCR: half-normal (detFun = 0), half-normal plateau (detFun = 1), exponential (detFun = 2), asymmetric logistic (detFun = 3), bimodal (detFun = 4) and donut (detFun = 5).

Usage

getHomeRangeArea(
  x = 2,
  detFun = 0,
  prob = 0.95,
  d = 6,
  xlim = c(0, 30),
  ylim = c(0, 30),
  nBreaks = 800,
  tol = 0.00001,
  nIter = 2000
)

Arguments

x	Vector or matrix (parameters in columns) of values for different parameters corresponding to the specified detection function.
detFun	Numeric vNumeric variable denoting the type of detection function. 0 = Half-normal, 1 = Half-normal plateau, 2 = Exponential, 3 = Asymmetric logistic, 4 = Bimodal, 5 = Donut.
prob	Numeric variable denoting the quantile probability to compute the home range radius.
d	Numeric variable giving an initial value of the radius.
xlim	Vector of length 2 giving the range along x-axis.
ylim	Vector of length 2 giving the range along y-axis.
nBreaks	Numeric variable denoting the number of breaks along an axis.
tol	Numeric variable denoting the allowed tolerance in the radius estimate.
nIter	Numeric variable giving the maximum number of iterations in bisection algorithm.

Author(s)

Soumen Dey

References

Dey, S., Bischof, R., Dupont, P. P. A., & Milleret, C. (2022). Does the punishment fit the crime? Consequences and diagnosis of misspecified detection functions in Bayesian spatial capture–recapture modeling. Ecology and Evolution, 12, e8600. https://doi.org/10.1002/ece3.8600

Examples

## Not run: 

# A user friendly vignette is also available on github: 
# https://github.com/nimble-dev/nimbleSCR/blob/master/nimbleSCR/vignettes/
# Vignette name: Fit_with_dbinomLocal_normalPlateau_and_HomeRangeAreaComputation.rmd

# HALF-NORMAL PLATEAU FUNCTION (detFun = 1) 
habitatMask <- matrix(1, nrow = 30, ncol= 30, byrow = TRUE)

prob <- 0.95
paramnames.hr <- c("HRradius", "HRarea")
sigma <- 1
w <- 1.5
params <- c(sigma, w)
names(params) <- c("sigma", "w")
HRAnim <- getHomeRangeArea( x = params, detFun = 1, prob = prob, d = 6,
                      xlim = c(0, dim(habitatMask)[2]), ylim = c(0, dim(habitatMask)[1]),
                      nBreaks = 800, tol = 1E-5, nIter = 2000)

# Different values of argument "detFun"
# 0 = Half-normal, 1 = Half-normal plateau, 2 = Exponential,
# 3 = Aysmmetric logistic, 4 = Bimodal, 5 = Donut.
HR.hnp <- c(HRAnim$run())
names(HR.hnp) <- paramnames.hr
print(HR.hnp)
# FASTER HRA COMPUTATION USING NIMBLE
samples <- cbind(rgamma(n = 500, shape = 1, rate = 1), rgamma(n = 500, shape = 1.5, rate = 1))
colnames(samples) <- c("sigma", "w")
HRAnim.mat <- getHomeRangeArea(x = samples, detFun = 1, prob = prob, d = 6, 
                         xlim = c(0, dim(habitatMask)[2]), ylim = c(0, dim(habitatMask)[1]),
                         nBreaks = 800, tol = 1E-5, nIter = 2000)

cHRAnim.arr <- compileNimble(HRAnim.mat, resetFunctions = TRUE)

HRA.Runtime <- system.time(
  HR.chain <- cHRAnim.arr$run()
)
print(HRA.Runtime)
dimnames(HR.chain)[[2]] <- paramnames.hr
HRest <- do.call(rbind, lapply(c(1:2), function(j){
  c(mean(HR.chain[,j], na.rm = TRUE), sd(HR.chain[,j], na.rm = TRUE))
}))
dimnames(HRest) <- list(paramnames.hr, c("MEAN", "SD"))

cat("Numerical estimates using MCMC samples: \n", sep = "")
print(HRest)

# HALF-NORMAL FUNCTION (detFun = 0) 
sigma = 2
params <- c(sigma)
names(params) <- c("sigma")

HRAnim <- getHomeRangeArea(x = params, detFun = 0, prob = prob, d = 6, 
                     xlim = c(0, dim(habitatMask)[2]), ylim = c(0, dim(habitatMask)[1]),
                     nBreaks = 800, tol = 1E-5, nIter = 2000)

HR.hn <- c(HRAnim$run())
names(HR.hn) <- paramnames.hr
print(HR.hn)

# Exponential (detFun = 2) 

rate = 1/2
params <- c(rate)
names(params) <- c("rate")
HRAnim <- getHomeRangeArea(x = params, detFun = 2, prob = prob, d = 6, 
                     xlim = c(0, dim(habitatMask)[2]), ylim = c(0, dim(habitatMask)[1]),
                     nBreaks = 800, tol = 1E-5, nIter = 2000)
HR.exp <- c(HRAnim$run())
names(HR.exp) <- paramnames.hr
print(HR.exp)

# Asymmetric logistic (detFun = 3) 

sigma = 2
alpha.a = 5 
alpha.b = 1
params <- c(sigma, alpha.a, alpha.b)
names(params) <- c("sigma", "alpha.a", "alpha.b")
HRAnim <- getHomeRangeArea(x = params, detFun = 3, prob = prob, d = 6, 
                     xlim = c(0, dim(habitatMask)[2]), ylim = c(0, dim(habitatMask)[1]),
                     nBreaks = 800, tol = 1E-5, nIter = 2000)
HR.al <- c(HRAnim$run())
names(HR.al) <- paramnames.hr
print(HR.al)


# Bimodal (detFun = 4) 

p0.a = 0.25
sigma.a = 0.5
p0.b = 0.15 
sigma.b = 1
w = 2
params <- c(sigma.a, sigma.b, p0.a, p0.b, w)
names(params) <- c("sigma.a", "sigma.b", "p0.a", "p0.b", "w")
HRAnim <- getHomeRangeArea(x = params, detFun = 4, prob = prob, d = 6, 
                     xlim = c(0, dim(habitatMask)[2]), ylim = c(0, dim(habitatMask)[1]),
                     nBreaks = 800, tol = 1E-5, nIter = 2000)
HR.bi <- c(HRAnim$run())
names(HR.bi) <- paramnames.hr
print(HR.bi)

# Donut (detFun = 5) 

sigma.a = 1.5 
sigma.b = 1 
w = 1 
params <- c(sigma.a, sigma.b, w)
names(params) <- c("sigma.a", "sigma.b", "w")
HRAnim <- getHomeRangeArea(x = params, detFun = 5, prob = prob, d = 6, 
                     xlim = c(0, dim(habitatMask)[2]), ylim = c(0, dim(habitatMask)[1]),
                     nBreaks = 800, tol = 1E-5, nIter = 2000)
HR.dn <- c(HRAnim$run())
names(HR.dn) <- paramnames.hr
print(HR.dn)


## End(Not run)

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