Make a lineage through time (LTT) plot

lttPlot plots the lineage through time (LTT) of a phylo object. It also adds a reference line connecting the edges of the graph.

Usage

lttPlot(
  phy,
  lwd = 1,
  col = "red",
  plot = TRUE,
  rel.time = FALSE,
  add = FALSE,
  knitr = FALSE
)

Arguments

phy

A phylo object, as specified by the ape package.

lwd

Line width.

col

Line color.

plot

A logical indicating with calculations should be plotted. If FALSE, function returns a list of the calculated points.

rel.time

A logical indicating how the time scale should be shown. If FALSE (default), plots the absolute time since phy's crown age. If TRUE, plots time as a relative proportion between crown age and furthest tip from root.

add

A logical indicating if plot should be added to pre-existing plot. Default is FALSE.

knitr

Logical indicating if plot is intended to show up in RMarkdown files made by the Knitr R package.

Value

Plots the sum of alive lineages per point in time, and adds a red line as a reference of expectation under pure birth. If plot = FALSE, a list the richness of each point in time, and phy's crown age.

References

Paradis, E. (2012). Analysis of Phylogenetics and Evolution with R (Vol. 2). New York: Springer.

See also

Other macroevolution: calcFossilDivTT(), checkAndFixUltrametric(), countSeqDiffs(), estimateSpeciation(), fitCRBD(), plotPaintedWhales(), plotProteinSeq(), plotRawFossilOccs(), simulateBirthDeathRich(), simulateTree()

Author

Daniel Rabosky, Matheus Januario, Jennifer Auler

Examples

S <- 1
E <- 0
set.seed(1)
phy <- simulateTree(pars = c(S, E), max.taxa = 20, max.t = 5)
lttPlot(phy, knitr = TRUE)

lttPlot(phy, plot = FALSE, knitr = TRUE)
#> $ldata
#>            stime  lineages
#>  [1,] 0.00000000 0.6931472
#>  [2,] 0.06989763 1.0986123
#>  [3,] 0.15597366 1.3862944
#>  [4,] 0.60566076 1.6094379
#>  [5,] 0.71359732 1.7917595
#>  [6,] 0.75750071 1.9459101
#>  [7,] 0.86636212 2.0794415
#>  [8,] 1.01919949 2.1972246
#>  [9,] 1.13422660 2.3025851
#> [10,] 1.37067812 2.3978953
#> [11,] 1.42212044 2.4849066
#> [12,] 1.47034648 2.5649494
#> [13,] 1.50608706 2.6390573
#> [14,] 1.51820710 2.7080502
#> [15,] 1.58208936 2.7725887
#> [16,] 1.66461861 2.8332133
#> [17,] 1.71894482 2.8903718
#> [18,] 1.74853490 2.9444390
#> [19,] 1.80376852 2.9957323
#> 
#> $age
#> [1] 1.855181
#>