rase (version 0.3-2)

data.for.3d:

Description

Takes the output from a rase run, the corresponding phylogenetic tree and tip polygonal distributions to create and object used for the different 3D plotting functions.

Usage

data.for.3d(res, tree, polygons)

Arguments

res

the output file from a rase run.

tree

phylogenetic tree of class "phylo" used as input for rase.

polygons

list of polygons in owin.object format used as input for rase.

Value

Returns an object required by the plotting functions phylo.3d, add.dens and add.polygons. It is efectively a list with the following elements: $xyz containing the 3D coordinates, $edge containing the tree$edge and $pol containing the polygons.

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

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

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))
#   
## ---------------------------------------------