localize_classic: Prepare classic SCR data components for local modeling...

In sitkensis22/localSCR: Supporting functions for advanced Bayesian spatial capture-recapture modeling using 'nimble'

Prepare classic SCR data components for local modeling approach

Description

A function to scale up from individual-level state-space to study-area level state-space using classic SCR data components.

Usage

localize_classic(
  y,
  grid_ind,
  X,
  crs_,
  sigma_,
  s.st,
  site = NULL,
  hab_mask = FALSE
)

Arguments

y	Either a matrix or array of encounter history data, possibly from sim_classic().
grid_ind	A matrix representing an individual state-space grid. This is returned from grid_classic.
X	Either a matrix or array representing the coordinates of traps in UTMs. An array is used when traps are clustered over a survey area.
crs_	The UTM coordinate reference system (EPSG code) used for your location provided as an integer (e.g., 32608 for WGS 84/UTM Zone 8N).
sigma_	The scaling parameter of the bivariate normal kernel either in meters or kilometers as an integer. Note that if sigma_ is sex-specific, the maximum value will be used.
s.st	A matrix of starting activity center coordinates. This is returned from initialize_classic.
site	Either NULL (if a 2D trap array is used) or a vector of integers denoting which trap array an individual (either detected or augmented) belongs to. Note that site is provided from sim_classic when a 3D trap array is used. However, this site variable must be correctly augmented based on the total augmented population size (i.e., M).
hab_mask	Either FALSE (the default) or a matrix or array output from mask_polygon or mask_raster functions.

Details

This function converts classic SCR data to a format that is used in local evaluations of the individual state-space.

Value

A list of data components needed to for classic SCR models in a local approach. Specifically, the function returns:

• y Individual-specific encounter history that only considers traps within a distance of 9 times sigma_.

• X Individual-specific trap array that only provides coordinates for traps within a distance of 9 times sigma_.

• grid A matrix or array of state-space grid coordinates that encompasses all individual state-space grids.

• prop_habitat The proportion of suitable habitat for each individual. Note that this is only returned when a habitat mask is used.

• ext_mat A matrix of individual state-space grid extents.

• ext An Extent object from the raster package for the scaled-up state-space grid.

• Jind A vector with the number of traps each individual is exposed to.

• s.st A matrix of starting activity center coordinates.

Author(s)

Daniel Eacker

Examples

## Not run: 
# simulate a single trap array with random positional noise
x <- seq(-1600, 1600, length.out = 6)
y <- seq(-1600, 1600, length.out = 6)
traps <- as.matrix(expand.grid(x = x, y = y))
# add some random noise to locations
traps <- traps + runif(prod(dim(traps)),-20,20) 
mysigma = 300 # simulate sigma of 300 m
mycrs = 32608 # EPSG for WGS 84 / UTM zone 8N
pixelWidth = 100 # grid resolution

# Create initial grid and extent (use a slightly bigger buffer to match
# scaled-up state-space below)
Grid = grid_classic(X = traps, crs_ = mycrs, buff = 3.7*mysigma, res = pixelWidth)

# Simulated abundance
Nsim = 250

# simulate SCR data
data3d = sim_classic(X = traps, ext = Grid$ext, crs_ = mycrs, 
sigma_ = mysigma, prop_sex = 1, N = Nsim, K = 4, base_encounter = 0.15, 
enc_dist = "binomial", hab_mask = FALSE, setSeed = 50)

# generate initial activity center coordinates for 2D trap array without 
# habitat mask
s.st = initialize_classic(y=data3d$y, M=500, X=traps, ext = Grid$ext, 
hab_mask = FALSE, all_random = FALSE)

# now use grid_classic to create an individual-level state-space (with origin 0, 0)
Grid_ind = grid_classic(X = matrix(c(0,0),nrow=1), crs_ = mycrs, 
          buff = 3*mysigma, res = 100)

# now localize the data components created above
local_list = localize_classic(y = data3d$y, grid_ind = Grid_ind$grid, X=traps, 
                           crs_ = mycrs, sigma_ = mysigma, s.st = s.st,
                           site = NULL, hab_mask = FALSE)
# inspect local list
str(local_list)

## End(Not run)

sitkensis22/localSCR documentation built on May 15, 2022, 5:26 p.m.