pdRaster: Probability of origin surfaces

Description

Calculate posterior probabilities of origin for a sample based on its isotope ratio.

Usage

pdRaster(r, unknown, prior = NULL, mask = NULL, genplot = TRUE, outDir = NULL)

Value

RasterStack or RasterLayer including a probability density surface for each individual in unknown. If outDir is not NULL, writes individual rasters in GeoTIFF format and a single PDF file with images for each probability density raster to the designated directory.

Arguments

r: RasterStack or RasterBrick with two layers, rescale object (see calRaster), or isoStack object. For user-generated raster objects, the first layer must be the substrate-specific isoscape (mean prediction) and the second the isoscape prediction uncertainty (1 standard deviation).
unknown: data.frame, refTrans object, or list of two or more refTrans objects. For user-created data.frame, first column should contain unique sample IDs, and subsequent columns should contain sample isotope values for one or more isotopes to be used in assignment.
prior: raster. Optional raster layer with prior probabilities, which has the same projection, resolution and extent as r.
mask: SpatialPolygonsDataFrame. This mask will constrain the assignment area. If this is not provided, a default of mask of the extent of r is used.
genplot: logical. Plot results in R.
outDir: character string. Directory path to which output will be saved. If NULL no files are written.

Details

If more than one isotope marker is to be used for multivariate assignment, r must be an isoStack object and the number of isoscapes in that object must be equal to the number of isotope-value columns or refTrans objects included in unknown. Isoscapes and unknown sample values will be matched based on order, so it is critical that the values appear in the same order in these two input objects.

Examples

Run this code

# load North America boundary and global isoscape
data("naMap")
data("d2h_lrNA")

# load hydrogen isotope data for human hair in North America
d = subOrigData(group = "Modern human", mask = naMap)

# rescale from environmental isoscape to tissue isoscape
r = calRaster(known = d, isoscape = d2h_lrNA, mask = naMap)

# sample to assign
id = "smile"
d2H = -80
un = data.frame(id, d2H)

# posterior probability surface
asn = pdRaster(r, unknown = un, mask = naMap)