5 \title{Lineages Through Time Plot}
7 ltt.plot(phy, xlab = "Time", ylab = "N", ...)
9 mltt.plot(phy, ..., dcol = TRUE, dlty = FALSE,
10 legend = TRUE, xlab = "Time", ylab = "N")
13 \item{phy}{an object of class \code{"phylo"}; this could be an object
14 of class \code{"multiPhylo"} in the case of \code{mltt.plot}.}
15 \item{xlab}{a character string (or a variable of mode character)
16 giving the label for the x-axis (default is "Time").}
17 \item{ylab}{idem for the y-axis (default is "N").}
18 \item{...}{in the cases of \code{ltt.plot()} and \code{ltt.lines()}
19 these are further (graphical) arguments to be passed to
20 \code{plot()} or \code{lines()}, respectively (see \code{Details:}
21 on how to transform the axes); in the case \code{mltt.plot()} these
22 are additional trees to be plotted (see \code{Details:}).}
23 \item{dcol}{a logical specifying whether the different curves should
24 be differentiated with colors (default is \code{TRUE}).}
25 \item{dlty}{a logical specifying whether the different curves should
26 be differentiated with patterns of dots and dashes (default is
28 \item{legend}{a logical specifying whether a legend should be
32 These functions plot, on the current graphical device, the minimum
33 numbers of lineages through time from phylogenetic trees.
36 \code{ltt.plot} does a simple lineages through time (LTT)
37 plot. Additional arguments (\code{...}) may be used to change, for
38 instance, the limits on the axes (with \code{xlim} and/or
39 \code{ylim}) or other graphical settings (\code{col} for the color,
40 \code{lwd} for the line thickness, \code{lty} for the line type may be
41 useful; see \code{\link[graphics]{par}} for an exhaustive listing of
42 graphical parameters). The \eqn{y}-axis can be log-transformed by
43 adding the following option: \code{log = "y"}.
45 \code{ltt.lines} adds a LTT curve to an existing plot. Additional
46 arguments (\code{...}) may be used to change the settings of the added
47 line. Of course, the settings of the already existing LTT plot cannot
50 \code{mltt.plot} does a multiple LTT plot taking as arguments one or
51 several trees. These trees may be given as objects of class
52 \code{"phylo"} (single trees) or \code{"multiPhylo"} (multiple
53 trees). Any number of objects may be given. This function is mainly
54 for exploratory analyses with the advantages that the axes are set
55 properly to view all lines, and the legend is plotted by default. For
56 more flexible settings of line drawings, it is probably better to
57 combine \code{ltt.plot()} with successive calls of \code{ltt.lines()}
58 (see \code{Examples:}).
61 Harvey, P. H., May, R. M. and Nee, S. (1994) Phylogenies without
62 fossils. \emph{Evolution}, \bold{48}, 523--529.
64 Nee, S., Holmes, E. C., Rambaut, A. and Harvey, P. H. (1995) Inferring
65 population history from molecular phylogenies. \emph{Philosophical
66 Transactions of the Royal Society of London. Series B. Biological
67 Sciences}, \bold{349}, 25--31.
69 \author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}}
71 \code{\link{skyline}}, \code{\link{branching.times}},
72 \code{\link{birthdeath}}, \code{\link{bd.ext}}, \code{\link{yule.cov}}
73 \code{\link[graphics]{plot}} for the basic plotting function in R
78 opar <- par(mfrow = c(2, 1))
79 ltt.plot(bird.families)
80 title("Lineages Through Time Plot of the Bird Families")
81 ltt.plot(bird.families, log = "y")
82 title(main = "Lineages Through Time Plot of the Bird Families",
83 sub = "(with logarithmic transformation of the y-axis)")
85 ### to plot the tree and the LTT plot together
86 layout(matrix(1:4, 2, 2))
87 plot(bird.families, show.tip.label = FALSE)
88 ltt.plot(bird.families, main = "Bird families")
89 plot(bird.orders, show.tip.label = FALSE)
90 ltt.plot(bird.orders, main = "Bird orders")
92 mltt.plot(bird.families, bird.orders)
93 ### Generates 10 random trees with 23 tips:
94 TR <- replicate(10, rcoal(23), FALSE)
95 ### Give names to each tree:
96 names(TR) <- paste("random tree", 1:10)
97 ### And specify the class of the list so that mltt.plot()
98 ### does not trash it!
99 class(TR) <- "multiPhylo"
100 mltt.plot(TR, bird.orders)
101 ### And now for something (not so) completely different:
102 ltt.plot(bird.orders, lwd = 2)
103 for (i in 1:10) ltt.lines(TR[[i]], lty = 2)
104 legend(-10, 5, lwd = c(2, 1), lty = c(1, 2), bty = "n",
105 legend = c("Bird orders", "Random trees"))