rase (version 0.2-22)

add.dens: Plot the Posterior Density for each Ancestor in 3D Space

Description

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).

Usage

add.dens(df3, res, nlevels = 20, z.scale = 1, col = c(1:nnode), ...)

Arguments

df3

an object from data.for.3d.

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., nlevels = 10 will plot the 90% CI, nlevels = 20 (the default) will plot the 95% CI).

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 phylo.3d

col

vector of colors for the polygons.

...

further arguments to be passed to polygon3d.

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

data.for.3d, phylo.3d, add.polygons

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
# 
# if(requireNamespace("rpanel") && requireNamespace("tcltk"))
#   add.dens(df3, mcmc, z.scale = 10, col = c(2:8))
# ## End(Not run)