ratioOverlap: Calculate the proportion of a range area that is either 1:...

In cmerow/changeRangeR: Change Metrics for Species Geographic Ranges

Calculate the proportion of a range area that is either 1: contained by geographic categories, or 2: correlated with a continuous environmental layer.

Description

Calculate the proportion of the species' range (e.g., a thresholded SDM) that is contained by landcover categories taken from a shapefile. Example shapefile categories include protected areas, threatened areas. ratioOverlap returns a list of the masked raster layer and the percent of the total range that lies within the shapefile polygons specified. If shp is a raster representing an environmental layer, the proportion of presence within quantiles of the environmental layer and the correlation between the layer and the range are returned.

Usage

ratioOverlap(
  r,
  shp = NULL,
  rasMask = NULL,
  field = NULL,
  category = NULL,
  subfield = FALSE,
  quant = "quartile"
)

Arguments

r	either categorical raster or shapefile object representing a binary range.
shp	either 1) a shapefile of land cover features or 2) a continuous raster. Must be in same projection as r parameter. If shp is a raster, then the number of cells within each quantile are calculated.
rasMask	(optional) a raster layer to calculate the Pearson correlation with the object r. Only if r or shp is a raster layer.
field	The shapefile field attribute containing the features to compare (i.e., the column name).
category	a list of the names of shapefile features to compare. If all features are to be used, input "All".
subfield	boolean. If TRUE, the overlap ratio of all unique categories of shp will be calculated.
quant	Either the character string "quartile" for the ratio of each quartile, or a concatenation of values to use instead.

Value

a list of three objects. The first object is a raster object showing the masked range. The second is a character showing the percentage of range within the category of interest. The third shows the correlation with rasMask if it is supplied.

Examples

# create binary raster
r <- raster::raster(nrows=108, ncols=108, xmn=-50, xmx=50)
raster::values(r)<- runif(n = (108*108))
r[r < 0.5] <- NA
r[r > 0.5] <- 1
# create shp
shp <- raster::raster(nrows=108, ncols=108, xmn=-50, xmx=50)
raster::values(shp)<- runif(n = (108*108))
# ratioOverlap
ratioOverlap(r = r, shp = shp)

cmerow/changeRangeR documentation built on Feb. 13, 2024, 8:01 a.m.