divCurveFossilRecordSim: Diversity-Curve Plotting for Simulations of Diversification...
In paleotree: Paleontological and Phylogenetic Analyses of Evolution

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/divCurveFossilRecordSim.R

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.

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

`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.

This function is essentially a wrapper for paleotree function multiDiv.

This function returns nothing: it just creates a plot.

David W. Bapst

simFossilRecord

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)