coverage_plot: coverage_plot

In richardjtelford/palaeoSig: Significance Tests for Palaeoenvironmental Reconstructions

coverage_plot

Description

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

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.

Value

A ggplot object.

Examples

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 March 16, 2023, 8:08 a.m.