ltt.plot {ape} | R Documentation |
This function plots, on the current graphical device, the minimum numbers of lineages through time from a phylogenetic tree.
ltt.plot(phy, ...)
phy |
an object of class "phylo" . |
... |
further arguments to be passed to plot() (see
Details: on how to transform the axes). |
The y-axis can be log-transformed by adding the following
option: log = "y"
.
Emmanuel Paradis paradis@isem.univ-montp2.fr
Harvey, P. H., May, R. M. and Nee, S. (1994) Phylogenies without fossils. Evolution, 48, 523529.
Nee, S., Holmes, E. C., Rambaut, A. and Harvey, P. H. (1995) Inferring population history from molecular phylogenies. Philosophical Transactions of the Royal Society of London. Series B. Biological Sciences, 349, 2531.
skyline
, branching.times
,
birthdeath
, plot
for the basic
plotting function in R
data(bird.families) data(bird.orders) opar <- par(mfrow = c(2, 1)) ltt.plot(bird.families) title("Lineages Through Time Plot of the Bird Families") ltt.plot(bird.families, log = "y") title(main = "Lineages Through Time Plot of the Bird Families", sub = "(with logarithmic transformation of the y-axis)") par(opar) ### to plot the tree and the LTT plot together tmp <- bird.families tmp$tip.label <- rep("", length(bird.families$tip.label)) tmp2 <- bird.orders tmp2$tip.label <- rep("", length(bird.orders$tip.label)) layout(matrix(1:4, 2, 2)) plot(tmp) ltt.plot(bird.families, main = "Bird families") plot(tmp2) ltt.plot(bird.orders, main = "Bird orders")