add.timeframe: High-lighting ages in chronograms

In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description

This function ...

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

Author(s)

Christoph Heibl

See Also

add.geoscale, read.beast, 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
# -------------------
plot.phylo.upon(bird.orders)
	

fmichonneau/phyloch documentation built on May 16, 2019, 1:45 p.m.