divCurveFossilRecordSim: Diversity-Curve Plotting for Simulations of Diversification...

In dwbapst/paleotree: Paleontological and Phylogenetic Analyses of Evolution

Diversity-Curve Plotting for Simulations of Diversification and Sampling In the Fossil Record

Description

An extremely simple plotting function, which plots the original taxonomic diversity versus the sampled taxonomic diversity, for use with output from the function simFossilRecord. If sampling processes were not included in the model, then it plots simply the single diversity curve.

Usage

divCurveFossilRecordSim(
  fossilRecord,
  merge.cryptic = TRUE,
  plotLegend = TRUE,
  legendPosition = "topleft",
  curveColors = c("black", "red"),
  curveLineTypes = c(1, 2)
)

Arguments

fossilRecord	A list object output by simFossilRecord, often composed of multiple elements, each of which is data for 'one taxon', with the first element being a distinctive six-element vector composed of numbers, corresponding to the six variable tables by fossilRecord2fossilTaxa after simulating with simFossilRecord (originally produced by deprecated function simFossilTaxa).
merge.cryptic	If TRUE, cryptic taxon-units (i.e. those in the same cryptic complex) will be merged into single taxa for the sake of being counted in the diversity curves presented by this function.
plotLegend	A logical. Should a legend be plotted? Only applies if sampling processes were modeled.
legendPosition	Where should the legend be plotted? See help for legend for details. Only applies if sampling processes were modeled.
curveColors	A vector of length two indicating what colors the original and sampled diversity curves should be displayed in. Only applies if sampling processes were modeled.
curveLineTypes	A vector of length two indicating what colors the original and sampled diversity curves should be displayed in. Only applies if sampling processes were modeled.

Details

This function is essentially a wrapper for paleotree function multiDiv.

Value

This function returns nothing: it just creates a plot.

Author(s)

David W. Bapst

See Also

simFossilRecord

Examples

set.seed(44)
record <- simFossilRecord(p = 0.1, q = 0.1, r = 0.1, nruns = 1,
	nTotalTaxa = c(20,30) ,nExtant = 0, plot = FALSE)

# now let's plot it
divCurveFossilRecordSim(record)

dwbapst/paleotree documentation built on July 9, 2024, 9:18 a.m.