Description Usage Arguments Value Author(s) References See Also Examples
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.
1 | data.for.3d(res, tree, polygons)
|
res |
the output file from a |
tree |
phylogenetic tree of class |
polygons |
list of polygons in |
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.
Petr Keil, Ignacio Quintero
Quintero, I., Keil, P., Jetz, W., Crawford, F. W. 2015 Historical Biogeography Using Species Geographical Ranges. Systematic Biology. doi: 10.1093/sysbio/syv057
phylo.3d
, add.dens
, add.polygons
, rase
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | # 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)
|
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