skylineplot {ape} | R Documentation

## Drawing Skyline Plot Graphs

### Description

These functions provide various ways to draw skyline plot graphs on the current graphical device. Note that `skylineplot(z, ...)` is simply a shortcut for `plot(skyline(z, ...))`. The skyline plot itself is an estimate of effective population size through time, and is computed using the function `skyline`.

### Usage

    ## S3 method for class 'skyline'
    plot(x, show.years=FALSE, subst.rate, present.year, ...)
    ## S3 method for class 'skyline'
    lines(x, show.years=FALSE, subst.rate, present.year, ...)
    skylineplot(z, ...)
    skylineplot.deluxe(tree, ...)

### Arguments

`x` | skyline plot data (i.e. an object of class `"skyline"`).
`z` | Either an ultrametric tree (i.e. an object of class `"phylo"`), or coalescent intervals (i.e. an object of class `"coalescentIntervals"`), or collapsed coalescent intervals (i.e. an object of class `"collapsedIntervals"`).
`tree` | ultrametric tree (i.e. an object of class `"phylo"`).
`show.years` | option that determines whether the time is plotted in units of of substitutions (default) or in years (requires specification of substution rate and year of present).
`subst.rate` | substitution rate (see option show.years).
`present.year` | present year (see option show.years).
`...` | further arguments to be passed on to `skyline()` and `plot()`.

### Details

See `skyline` for more details (incl. references) about the skyline plot method.

### Author(s)

Korbinian Strimmer

### See Also

`plot` and `lines` for the basic plotting function in R, `coalescent.intervals`, `skyline`

### Examples

    # get tree
    data("hivtree.newick") # example tree in NH format
    tree.hiv <- read.tree(text = hivtree.newick) # load tree

    #### classic skyline plot
    skylineplot(tree.hiv) # shortcut

    #### plot classic and generalized skyline plots and estimate epsilon
    sk.opt <- skylineplot.deluxe(tree.hiv)
    sk.opt$epsilon

    #### classic and generalized skyline plot ####
    sk1 <- skyline(tree.hiv)
    sk2 <- skyline(tree.hiv, 0.0119)

    # use years rather than substitutions as unit for the time axis
    plot(sk1, show.years=TRUE, subst.rate=0.0023, present.year = 1997, col=c(grey(.8),1))
    lines(sk2,  show.years=TRUE, subst.rate=0.0023, present.year = 1997)
    legend(.15,500, c("classic", "generalized"), col=c(grey(.8),1),lty=1)

    #### various skyline plots for different epsilons
    layout(mat= matrix(1:6,2,3,byrow=TRUE))
    ci <- coalescent.intervals(tree.hiv)
    plot(skyline(ci, 0.0));title(main="0.0")
    plot(skyline(ci, 0.007));title(main="0.007")
    plot(skyline(ci, 0.0119),col=4);title(main="0.0119")
    plot(skyline(ci, 0.02));title(main="0.02")
    plot(skyline(ci, 0.05));title(main="0.05")
    plot(skyline(ci, 0.1));title(main="0.1")
    layout(mat= matrix(1:1,1,1,byrow=TRUE))

[Package ape version 3.5 Index]