calc_highquality: Calculate quantiles and identify high-quality pixels for...

In tfullman/dia: Monte Carlo Development Simulation and Wildlife Impacts Analysis

Calculate quantiles and identify high-quality pixels for species raster

Description

calc_highquality is a helper function that prepares input data for the caribou and shorebird impact analyses (impact_caribou and impact_shorebird) by calculating quantiles of an input raster and determining the number of high-quality pixels (sensu Johnson et al. 2005). See Fullman et al. (in press) for details.

Usage

calc_highquality(x, y = NULL, z = NULL, wah = FALSE, sb = FALSE)

Arguments

x	A caribou calving resource selection function (RSF) or shorebird habitat suitability index (HSI) RasterLayer object.
y	Western Arctic Herd (WAH) caribou habitat overlap weighting RasterLayer object (optional).
z	Numeric value indicating the species-specific threshold value defining shorebird suitable habitat from habitat suitability values (from Saalfeld et al. 2013). Optional, only used if sb == TRUE.
wah	Logical indicator of whether the run is for the WAH. If so, adds the additional weighting analysis. Defaults to FALSE.
sb	Logical indicator of whether the run is for a shorebird. If so, adds a calculation of suitable habitat before calculating quantiles. Defaults to FALSE.

Value

data.frame object containing the 75% quantile value (quant75), number of high-quality pixels in the input raster (highquality.orig), and (if wah = TRUE) the weighted high-quality value (highquality.weighted).

References

Fullman TJ, Sullender BK, Cameron MD, Joly K. in press. Simulation modeling accounts for uncertainty while quantifying ecological effects of development alternatives. Ecosphere.

Johnson CJ, Boyce MS, Ray CL, Cluff DH, Gau RJ, Gunn A, Mulders R. 2005. Cumulative effects of human developments on arctic wildlife. Wildlife Monographs 160:1-36.

Saalfeld ST, Lanctot RB, Brown SC, Saalfeld DT, Johnson JA, Andres BA, Bart JR. 2013. Predicting breeding shorebird distributions on the Arctic Coastal Plain of Alaska. Ecosphere 4:16.

tfullman/dia documentation built on Oct. 17, 2023, 6:31 p.m.