data.for.3d: Transform Output for 3D Plotting

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

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.

Author(s)

Petr Keil, Ignacio Quintero

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))
  
## End(Not run)

ignacioq/rase documentation built on Feb. 20, 2022, 3:16 p.m.