ape (version 2.8)

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

Arguments

Details

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

See Also

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

Examples

Run this code
# 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))

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