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

In rase: Range Ancestral State Estimation for Phylogeography and Comparative Analyses

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.

Author(s)

Petr Keil

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
    add.dens(df3, mcmc, z.scale = 10, col = c(2:8))
  
## End(Not run)

rase documentation built on May 2, 2019, 12:46 p.m.