calcBinaryUse: Calculate binary use

In LandSciTech/caribouMetrics: Models and Metrics of Boreal Caribou Demography and Habitat Selection

Calculate binary use

Description

Convert continuous probability of use in each season to binary high use in any season or each season using thresholds given in a table.

Usage

calcBinaryUse(x, ...)

## S4 method for signature 'CaribouHabitat'
calcBinaryUse(x, tholdTable = threshTable, bySeason = FALSE)

Arguments

x	CaribouHabitat object where habitat use has been calculated, or a data.frame with columns PID, Spring, Summer, Fall, Winter, or a numeric vector containing ID values, in which case spring, summer, fall and winter must also be supplied
...	passed to methods
tholdTable	By default threshTable which contains thresholds determimed by Rempel (2021) using Youden's J and a false negative cost of 5. Change at own risk.
bySeason	logical. If FALSE (the default) the result is a single value of 1 when the habitat use was >= threshold in any season and 0 if not. If TRUE then the result is a 0 or 1 for each season.

Value

If bySeason is FALSE and x is a CaribouHabitat object then the result is 1 layer SpatRaster. If bySeason is TRUE and x is a CaribouHabitat object then the result is SpatRaster with a layer per season. If bySeason is FALSE and x is a data.frame then the result is a data.frame. If bySeason is TRUE and x is a data.frame then the result is a data.frame. If bySeason is FALSE and x is a vector then the result is a vector. If bySeason is TRUE and x is a vector then the result is a data.frame.

See Also

Caribou habitat functions: CaribouHabitat-class, caribouHabitat(), coefTableHR, coefTableStd, fnlcToResType, loadSpatialInputs(), plcToResType, rasterizeLineDensity(), reclassPLC(), resTypeCode, results(), rfuToResType, threshTable, updateCaribou()

Examples

# create example rasters
lc <- terra::rast(xmin = 0, xmax = 25000, ymin = 0, ymax = 25000, 
                     resolution = 250, crs = sf::st_crs(5070)$wkt)
lc[] <- 0
nd <- lc
nd[1:30, 1:30] <- 1
ad <- lc
ad[30:50, 3:50] <- 1
lc[] <- 1
lc[70:100, 70:100] <- 2



# create sf objects
lf <- sf::st_as_sf(sf::st_sfc(list(sf::st_linestring(matrix(c(0, 0, 10000, 10000),
                                                            ncol = 2, byrow = TRUE))),
                              crs = sf::st_crs(5070)))
esk <- sf::st_as_sf(sf::st_sfc(list(sf::st_linestring(matrix(c(0, 10000, 10000, 0),
                                                            ncol = 2, byrow = TRUE))),
                              crs = sf::st_crs(5070)))


projPol <- sf::st_sf(sf::st_as_sfc(sf::st_bbox(ad)))
projPol <- sf::st_set_crs(projPol, sf::st_crs(5070))

# calculate relative probability of use
res <- caribouHabitat(landCover = lc,
               linFeat = lf,
               esker = esk,
               natDist = nd,
               anthroDist = ad,
               projectPoly = projPol,
               caribouRange = "Nipigon",
               winArea = 1000 #leave as default NULL except for small examples
)
if(interactive()){
  plot(calcBinaryUse(res))
  plot(calcBinaryUse(res, bySeason = TRUE))
}

LandSciTech/caribouMetrics documentation built on Feb. 3, 2024, 9:41 p.m.