axisGeo: Geological Time Axis for Time-Calibrated Phylogenies

In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description

This function adds a geological time scale on the side of a phylogeny plot.

Usage

axisGeo(GTS, tip.time = 0, unit = c("epoch", "period"), ages = 
    TRUE, cex = 1, col = "white", texcol = "black", gridty = 0, 
    gridcol = "black")

Arguments

GTS	a data frame containing the geological time scale such as provided by strat2012.
tip.time	a real number giving time units back from present were the youngest taxa were sampled.
unit	a vector of mode character used to select geological time units that shall be displayed. When using gradstein04, "eon", "era", "period", "epoch", and "stage" are available.
ages	logical: if TRUE, a real-numbered axis of unit bounderies is added to the plot.
cex	a real number giving the character expansion.
col	a vector of mode character used to select background color(s). Will be recycled if necessary.
texcol	a vector of mode character used to select font color(s). Will be recycled if necessary.
gridty	an integer representing the line type of the grid exactly in the same way as lty argument in par: 0 or blank, 1 or "solid", 2 or "dashed", 3 or "dotted", 4 or "dotdash", 5 or "longdash", and 6 or "twodash".
gridcol	a vector of mode character used to select grid color(s). Will be recycled if necessary.

Details

This function is intended to make the geological time scale from the paleoPhylo package available to users of the ape package (paleoPhylo is not yet on CRAN). For more functions for analysing and plotting paleontological data, see the paleoPhylo package on R-Forge.

If the name of a time interval does not fit the space on the plotting device provided by that time frame, axisGeo tries to fit the name string by lowering the original character expansion. In order to avoid undiscernable small font sizes only character expansion of 50 percent or more of the original cex is allowed; in all other cases strings are abreviated and plotted with the original character expansion.

Author(s)

Christoph Heibl

References

Gradstein F.M., J.G. Ogg & A.G. Smith. 2004. A Geologic Time Scale. Cambridge University Press, Cambridge, UK. www.cambridge.org/uk/catalogue/catalogue.asp?isbn=0521786738.

International Commission on Stratigraphy. 2012. International stratigraphic chart: http://www.stratigraphy.org/upload/ISChart2009.pdf.

See Also

strat2012 for the current stratigraphic chart; gradstein04 (the 2004 stratigraphic chart from the paleoPhylo package) is still provided for backward comparison. axisPhylo, axisChrono, add.geoscale are further possibilities add axes to plotted phylogenies.

Examples

# phylogenetic relationships of bird orders:
# -----------------------------------------
data(bird.orders)
tr <- bird.orders

# Stratigraphic chart 2012
# ------------------------
data(strat2012)

# Classic:
# --------
plot.phylo(tr, edge.width = 2, label.offset = 0.5)
axisGeo(GTS = strat2012, unit = c("stage", "epoch", "period",
    "era"), cex = 0.8)

# You can impose a grid ...
# -------------------------
plot.phylo(tr, edge.width = 2, label.offset = 0.5)
axisGeo(GTS = strat2012, unit = "stage", col = c("grey80",
    "white"), gridty = 3)

# ... or use colors:
# ------------------
plot.phylo(tr, edge.width = 2, label.offset = 0.5)
axisGeo(GTS = strat2012, unit = "epoch", col = c("lightcyan",
    "lightpink"), texcol = "navy", gridty = 4, gridcol = "red")
	
# A tree with non-contemporaneous tips:
# -------------------------------------
# youngest tip:
yt <- 23.8

plot.phylo(tr, edge.width = 2, label.offset = 0.5)
axisGeo(strat2012, tip.time = yt, unit = c("stage", "epoch"))

# The same tree with tips pointing upward:
# ---------------------------------------------
par(mar = c(2,5,2,2)) # adjust left-hand margin
plot.phylo(tr, edge.width = 2, direction = "upward")
axisGeo(strat2012, tip.time = yt, unit = c("stage", "epoch"), 
	gridty = 3, gridcol = "red")

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