pdRaster: assign function

In SPATIAL-Lab/isorig: Rescale isoscape using known-origin tissue isotope values, and assign origin of unknown samples with isotopic data

Description

Assign unknown tissue isotope to calibrated precipitation isoscape.

Usage

pdRaster(r, prior =NULL, unknown, mask = NULL, genplot = T, saveFile = T)

Arguments

r	Output of calRaster, or RasterStack or RasterBrick with two layers. The tissue-calibrated isoscape raster (mean and sd) obtained from rescale function, or user provides
prior	raster. This is an optional raster layer with prior probabilities, which should has the same projection, resolution and extent as the isoscape raster.
unknown	data.frame. First column should be unique sample ID, and second column should be tissue d2H values of the individuals for which the assignments will be made.
mask	SpatialPolygonsDataFrame. This mask will constrain the assignment area. If this is not provided, a default of mask of rescaled.mean is used.
genplot	logical. Generate summary plots in R (TRUE [default]) or not (FALSE).
saveFile	logical. Save the results (TRUE [default]) or not (FALSE)).

Value

returns an object of class RasterStack or RasterLayer that includes a probability density raster for each individual in "unknown". pdRaster writes individual rasters in GTiff format to disk in the working directory for each individual in "unknown".

See Also

calRaster

Examples

data(naMap)
data(d2h_world)
d <- subOrigData(taxon = c("Homo sapiens"), mask = naMap)
r <- calRaster(known = d, isoscape = d2h_world, mask = naMap)
id <- "smile"
d2H <- -80
un <- data.frame(id,d2H)
asn <- pdRaster(r, unknown = un, mask=naMap)

SPATIAL-Lab/isorig documentation built on Aug. 13, 2019, 11:02 p.m.