plot.QA: PLot the quality assessment of the geographic assignment.

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

Description

Plot the output from QA results. Accuracy, precision and probability density of validation stations.

Usage

plot.QA(obj, savePDF = FALSE)

Arguments

obj	Either a single QA object or a list of QA objects
savePDF	logical. Save the plot as PDF (TRUE) or not (FALSE [default]).

References

Ma et al., 2019

Vander Zanden, H.B., Wunder, M.B., Hobson, K.A., Van Wilgenburg, S.L., Wassenaar, L.I., Welker, J.M. and Bowen, G.J., 2014. Contrasting assignment of migratory organisms to geographic origins using long-term versus year-specific precipitation isotope maps. Methods in Ecology and Evolution, 5(9), pp.891-900.

See Also

ggplot QA

Examples

# load data
data(naMap) # North America 
data(d2h_world) # precipitation hydrogen isotope of the world
data(bird_isotope) # oxygen and hydrogen isotopes of known-origin bird

# crop the world hydrogen data to North America
r <- crop(d2h_world, naMap)
plot(r)

# convert 2 standard deviation from d2h_world to 1 standard deviation
r[[2]] <- r[[2]]/2

# seperate the hydrogen isotope for the known-origin bird
bird_d2h <- bird[1:20,c("Longitude", "Latitude", "d2H")]
coordinates(bird_d2h) <- c(1,2)
proj4string(bird_d2h) <- proj4string(d2h_world)

# run quality assessment based hydrogen isotope from precipitation and known-origin bird
d2h_QA <- QA(isoscape = r, known = bird_d2h, valiStation = 2, 
                    valiTime = 5, setSeed = T)
                    
# plot the QA result
plot(d2h_QA)

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