rase (version 0.2-22)

add.polygons: Plot the Distributions for the Phylogenetic Tips in 3D

Description

Plots the polygon surfaces of the tips of the phylogeny. It is mapped in 3D space, where the x/y axes are longitude/latitude, and the z axis is time. Although it works by itself, the polygons are intended to overlay an existing phylo.3d plot (see example).

Usage

add.polygons(df3, axes = 2, ...)

Arguments

df3

an object from data.for.3d.

axes

number of axes to be plotted (1 = 'x', 2 = 'x' & 'y', 3 = 'x', 'y' & 'z').

...

further arguments to be passed to polygon3d.

Details

The polygons do not have to be non-overlapping, however, when they do, they “flicker”.

References

Quintero, I., Keil, P., Jetz, W., Crawford, F. W. 2015 Historical Biogeography Using Species Geographical Ranges. Systematic Biology. doi: 10.1093/sysbio/syv057

See Also

data.for.3d, phylo.3d, add.dens

Examples

# load the mcmc results from rase run, polygons and tree
data(rase_data, package = 'rase')

pnames <- c('dextralis', 'viridis', 'leucoptera', 'interjecta', 
'obscura', 'crepitans', 'ochroptera', 'napensis')
psophia_poly <- name.poly(psophia_poly, psophia_tree, poly.names = pnames)

# transform the data for 3d plotting
df3 <- data.for.3d(mcmc, psophia_tree, psophia_poly)

## Not run: 
# # plot the tree in 3D
# phylo.3d(df3, z.scale = 10, pts = TRUE)
# 
# # add the polygons representing the tip distributions
# add.polygons(df3)
# 
# # add the posterior density at each node of the 3d tree
# 
# if(requireNamespace("rpanel") && requireNamespace("tcltk"))
#   add.dens(df3, mcmc, z.scale = 10, col = c(2:8))
# ## End(Not run)