unionP: unionP

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

Description

Probability that at least one individual came from the location (union of probabilities)

Usage

unionP(pdR)

Arguments

pdR	probability density map which must be raster or RasterLayer

Examples

# load North America SpatialPolygonsDataFrame data in assignR package
data("naMap")
data(d2h_world)
d = subOrigData(taxon = c("Homo sapiens"), mask = naMap)
# Exclude some outliers. This step is optional, which depends on your data quality
d <-as.data.frame(d)
dd = d[d$coords.x1<(-80),]
dd <- SpatialPointsDataFrame(dd[,2:3], as.data.frame(dd[,1]))
crs(dd) <- "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"
# Rescale from environmental isoscape to tissue isoscape (known must be SpatialPointsDataFrame with coordinate reference system )
r = calRaster(known = dd, isoscape = d2h_world, mask = naMap)
# four unknown-origin example
id = c("A", "B", "C", "D")
d2H = c(-110, -180, -130, -150)
un = data.frame(id,d2H)
# assignment
asn = pdRaster(r,unknown=un,mask=naMap)
# Probability that at least one individual came from the location (union of probabilities)
unionP(asn)

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