Description Usage Arguments Author(s) References See Also Examples
Plots a user-specified credible interval from the posterior density for each ancestor according to rase results. 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 posterior densities are intended to overlay an existing phylo.3d
plot (see example).
1 |
df3 |
an object from |
res |
the output from a rase run. |
nlevels |
the credible interval to be plotted for every posterior probabilities. The nlevels is the inverse of the credible interval (CI) to be plotted (e.g., |
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 |
col |
vector of colors for the polygons. |
... |
further arguments to be passed to |
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
data.for.3d
, phylo.3d
, 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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