plot.QA {assignR}R Documentation

Plot quality metrics for geographic assignments

Description

Plot the output from QA, including spatial precision, bias, sensitivity and odds ratio of known locations for validation samples.

Usage

## S3 method for class 'QA'
plot(x, ..., outDir = NULL)

Arguments

x

One or more QA objects

...

Other arguments to be passed to plot

outDir

character string. Directory path to which output will be saved. If NULL no files are written.

References

Ma, C. et al. (2020) assignR : An R package for isotope-based geographic assignment. Methods in Ecology and Evolution 11 996–1001. doi: 10.1111/2041-210X.13426.

Vander Zanden, H. B. et al. (2014) Contrasting assignment of migratory organisms to geographic origins using long-term versus year-specific precipitation isotope maps. Methods in Ecology and Evolution 5 891–900. doi: 10.1111/2041-210X.12229

See Also

QA

Examples

# load data
data("naMap") # North America 
data("d2h_lrNA") # precipitation hydrogen isoscape of North America
data("knownOrig") # isotopes of known-origin samples

# extract some known-origin data
d1 = subOrigData(taxon = "Buteo lagopus")

# run quality assessment based on precipitation hydrogen isotopes and 
# known-origin samples; small values of valiStation and valiTime 
# are used in example to reduce run time

# first with one example
# gives warning because a small number of samples are available
qa1 = QA(isoscape = d2h_lrNA, known = d1, valiStation = 1, 
          valiTime = 2, by = 10, mask = naMap, name = "Buteo")
                    
# plot the qa result
plot(qa1)

# now compare with a second data set
d2 = subOrigData(taxon = "Charadrius montanus")
qa2 = QA(isoscape = d2h_lrNA, known = d2, valiStation = 1, 
          valiTime = 2, by = 10, mask = naMap, name = "Charadrius")
plot(qa1, qa2)

[Package assignR version 2.1.0 Index]