add.timeframe: Highlight Age Intervals in Chronogram

In heibl/viper: VIsualitaion of Phylogenetics and Evolution with R

Description

Highlight age intervals in a chronogram.

Usage

add.timeframe(phy, age, clade = NULL, tips = NULL, ...)

Arguments

phy	An object of class phylo.
age	A vector of mode "numeric" giving an age or an age range.
clade	An integer giving the the node number of the MRCA of a clade to which the timeframe should be restricted.
tips	A vector of integers giving the numbers of tips to which the time frame should be restricted. Can be used for non-monophyletic groups.
...	Further arguments.

Value

None, add.timeframe is called for its side effects.

See Also

add.geoscale, noi

Examples

# phylogentic relationships of bird orders:
data(bird.orders)

# plot tree:
# setting edge and tip colors to zero (invisible) improves
# resolution 
plot(bird.orders, edge.color = 0, tip.color = 0)

# highlight some geological event, etc. ...
add.timeframe(bird.orders, age = c(12, 14), col = "skyblue",
              border = NA)
              
# restrict to certain clade ...
cl <- noi(bird.orders, c("Struthioniformes", "Anseriformes"))

add.timeframe(bird.orders, age = c(16:21), col = "pink",
              border = NA, clade = cl)
              
# or to some other non-monophyletic assemby:
add.timeframe(bird.orders, age = c(17:24), col = "yellow",
              border = NA, tips = 6:8)

# now plot tree again:
# arguments must be exactly the same of course, except for
# edge and tip colors
plotPhyloUpon(bird.orders)

heibl/viper documentation built on May 21, 2019, 10:47 a.m.