PlotModel2D: Create a 2D plot for a given model

In bomeara/phrapl: Phylogeography using Approximate Likelihood

Description

This creates a two-dimensional model

Usage

PlotModel2D(migrationIndividual, parameterVector=NULL, taxonNames=NULL,
	pad.for.input=FALSE, tree.lwd=30, tree.col="black", arrow.lwd=1,
	arrow.col="red", arrow.lty="solid", tip.cex = 1, tip.col = "black")

Arguments

migrationIndividual	This is the chosen model. If you want model 17 from migrationArray, you could pass this in as migrationIndividual=migrationArray[[17]]
parameterVector	If you have numeric parameter estimates, you can pass them in here. This affects things like node height, migration rate arrow width, etc. Otherwise, it will plot a generic model.
taxonNames	If instead of population A, B, ... you want Oahu, Hawaii, ... you can pass them in as a vector.
pad.for.input	[not implemented yet]
tree.lwd	Line width for the tree
tree.col	Color for the tree
arrow.lwd	Line width for migration arrows
arrow.col	Color for migration arrows
arrow.lty	Line type for migration arrows
tip.cex	Specify tip size
tip.col	Specify tip color

Details

This will create a plot showing migration, population collapse, and other features. It does not yet use parameter estimates. It shows a gradient for branches at the base of the tree to represent the history being lost in the mists of time.

Value

Creates a stunning image.

Author(s)

Brian O'Meara

See Also

SaveMovie, ~~~

Examples

data(MigrationArray_3pops_maxMigrationK1)
pretty.model <- migrationArray[[1]]
PlotModel2D(pretty.model)

bomeara/phrapl documentation built on Feb. 8, 2021, 6:45 p.m.