Description Usage Arguments Author(s) References See Also Examples
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).
1 |
df3 |
an object from |
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 |
pts |
if |
... |
further arguments to be passed to |
Petr Keil
Quintero, I., Keil, P., Jetz, W., Crawford, F. W. 2015 Historical Biogeography Using Species Geographical Ranges. Systematic Biology. doi: 10.1093/sysbio/syv057
data.for.3d
, add.dens
, add.polygons
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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