rase (version 0.2-22)

phylo.3d: Plots a Phylogenic Tree in 3D

Description

Plots a phylogenetic tree in 3D using rgl. It is mapped in 3D space, where the x/y axes are longitude/latitude, and the z axis is time. It is used as the first plot function to visualize the results of rase with add.dens and add.polygons (see example).

Usage

phylo.3d(df3, z.scale = 1, pts = TRUE, ...)

Arguments

df3

an object from data.for.3d.

z.scale

the scale of the time axis (vertical axis). Effectively, the time variable is multiplied by this number. It is very useful for visualization purposes. It should correspond with the z.scale argument in add.dens.

pts

if TRUE, points in the verices are plotted.

...

further arguments to be passed to lines3d.

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, add.dens, add.polygons

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)