Description Usage Arguments Details Author(s) References See Also Examples
Plots the polygon surfaces of the tips of the phylogeny. It is mapped in 3D space, where the x/y axes are longitude/latitude, and the z axis is time. Although it works by itself, the polygons are intended to overlay an existing phylo.3d
plot (see example).
1 | add.polygons(df3, axes = 2, ...)
|
df3 |
an object from |
axes |
number of axes to be plotted (1 = 'x', 2 = 'x' & 'y', 3 = 'x', 'y' & 'z'). |
... |
further arguments to be passed to |
The polygons do not have to be non-overlapping, however, when they do, they “flicker”.
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
, phylo.3d
, add.dens
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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