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