oddsRatio: oddsRatio

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

Description

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

Usage

oddsRatio(pdR, inputP)

Arguments

pdR	probability density map which must be raster or RasterLayer
inputP	points or polygons which must be data.frame or SpatialPolygons

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)

# Create SpatialPolygons with two polygons
p1 <- c(-100,60,-100,65,-110,65,-110,60,-100,60)
p1 <- matrix(p1, 5,2, byrow = T)
p1 <- Polygon(p1)
p1 <- Polygons(list(p1), "p1")
p2 <- c(-100,40,-100,45,-110,45,-110,40,-100,40)
p2 <- matrix(p2, 5,2, byrow = T)
p2 <- Polygon(p2)
p2 <- Polygons(list(p2), "p2")
p12 <- SpatialPolygons(list(p1,p2),1:2)
plot(p12)
# Calculate odds ratio for the two polygons created above
oddsRatio(asn, p12)

# points
pp1 <- c(-100,45)
pp2 <- c(-100,60)
pp12 <- as.data.frame(rbind(pp1,pp2))
# Caculate odds ratio for the two points created above
oddsRatio(asn, pp12)

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