coverage_plot

A simple diagnostic plot showing the coverage of fossil taxa in modern calibration set

Usage

coverage_plot(spp, fos, n2_rare = 5, label = NULL)

Arguments

spp

data.frame of modern species abundances

fos

data.frame of fossil species abundances

n2_rare

numeric value of Hill's N2 below which species are highlighted as rare

label

numeric label taxa where maximum fossil abundance - maximum modern abundance > label. Defaults to NULL which does not add labels

Value

A ggplot object.

Details

Finds the maximum abundance of fossil taxa and plots this against the maximum abundance the taxa in the modern calibration set. Taxa with a Hill's N2 less than rare in the calibration set are highlighted in blue. Taxa absent from the calibration set are highlighted in red. If there are many taxa above the 1:1 line, or important fossil taxa have a low N2 in the calibration set, reconstructions should be interpreted with caution.

Examples

data("SWAP", package = "rioja")
data("RLGH", package = "rioja")
coverage_plot(spp = SWAP$spec, fos = RLGH$spec, n2_rare = 5, label = 0)