coverage_plot: coverage_plot

Description Usage Arguments Details Value Examples

View source: R/coverage.plot.r

Description

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

Usage

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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

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 highlighed 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.

Value

A ggplot object.

Examples

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

richardjtelford/palaeoSig documentation built on Dec. 28, 2019, 9:01 p.m.