rase (version 0.2-21)

random_rase3d: Apply rase to Randomly Generated Data

Description

Generates a random tree and random tip poygons using a convex hull. It runs rase and then plots the result (optional). It is mostly intended for illustration/ validation purposes.

Usage

random_rase3d(mean_x = 0, mean_y = 0, sigma2x = 1, sigma2y = 1,
		x_ext = c(0.1, 0.5), y_ext = c(0.1, 0.5), niter = 1e3, 
		logevery = 10, plot.3d = TRUE, zscale = 5, 
		pbtree.list = list(n = 10), 
		phylo.3d.list = list(df3, z.scale = zscale, pts = TRUE), 
		add.polygons.list = list(df3, axes = 2), ...)

Arguments

mean_x

mean of the Brownian Motion process on the x axis to be generated according to the tree. By default mean_x = 0.

mean_y

mean of the Brownian Motion process on the y axis to be generated according to the tree. By default mean_y = 0.

sigma2x

rate parameter of the Brownian Motion process on the x axis to be generated according to the tree. By default sigma2x = 1.

sigma2y

rate parameter of the Brownian Motion process on the y axis to be generated according to the tree. By default msgima2y = 0.

x_ext

this controls the mean diameter of the polygons to be generated on the x axis.

y_ext

this controls the mean diameter of the polygons to be generated on the y axis.

niter

iteration cycle to print current iteration. By default niter = 1000.

logevery

iteration cycle to print current iteration. By default logevery = 10.

plot.3d

If TRUE (default), a 3d plot is generated with the results

zscale

the scale of the time axis (vertical axis). Effectively, the time variable is multiplied by this number. It is very useful for visualization purposes.

pbtree.list

a list containing arguments to be passed to pbtree.

phylo.3d.list

a list containing arguments to be passed to phylo.3d.

add.polygons.list

a list containing arguments to be passed to add.polygons.

...

further arguments to be passed to add.dens.

Value

• returns the output of rase.

References

Quintero, I., Keil, P., Jetz, W., Crawford, F. W. 2015 Historical Biogeography Using Species Geographical Ranges. Systematic Biology.

See Also

rase, phylo.3d, add.dens, add.polygons

Examples

# run random_rase3d for 500 iterations
results_random <- random_rase3d(niter = 500)
	
# explore the results
str(results_random)