assignR (version 1.2.0)

oddsRatio: Odds ratio of points or regions

Description

Calculate ratio of odds for two locations (points or polygons)

Usage

oddsRatio(pdR, inputP)

Arguments

pdR

RasterStack or RasterBrick of probability density maps, e.g., as produced by calRaster. All layers must have common projection.

inputP

SpatialPoints or SpatialPolygons (or *DataFrame equivalent) of length 2

Examples

# NOT RUN {
library(sp)

# load North America boundary and global isoscape
data("naMap")
data("d2h_world")

# load hydrogen isotope data for human hair in North America
d = subOrigData(taxon = "Homo sapiens", 
  reference = "Ehleringer et al. 2008", mask = naMap)

# rescale from environmental isoscape to tissue isoscape
r = calRaster(known = d, isoscape = d2h_world, mask = naMap)

# four unknown-origin examples
id = c("A", "B", "C", "D")
d2H = c(-110, -90, -105, -102)
un = data.frame(id,d2H)

# assignment
asn = pdRaster(r, unknown = un, mask = naMap)

# SpatialPolygons for two regions of interest
data("states")
s1 = states[states$STATE_ABBR == "UT",]
s2 = states[states$STATE_ABBR == "NM",]
plot(naMap)
plot(s1, border = "red", add=TRUE)
plot(s2, border = "blue", add=TRUE)

# Get odds ratio for two regions using SpatialPolygon method
s12 = rbind(s1, s2)
oddsRatio(asn, s12)                     

# Create SpatialPoints for two points of interest
pp1 = c(-112,40)
pp2 = c(-105,33)
pp12 = SpatialPoints(coords = rbind(pp1,pp2), 
  proj4string=CRS("+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0"))
points(pp12, pch = 21, bg = "light blue")

# Get odds ratio for two points using SpatialPoints method
oddsRatio(asn, pp12)
# }