plot.ancestralCauchy function

Plot for class ancestralCauchy

This function takes an object of class ancestralCauchy, result of function ancestral or increment, and plots the reconstructed states for given nodes.

## S3 method for class 'ancestralCauchy'
plot(x, node, n_col, intervals = NULL, ...)

Arguments

• x: an object of class ancestralCauchy, result of function ancestral or increment.

• node: the vector of nodes where to plot the ancestral reconstruction. Can be missing, in which case all the nodes reconstructed in the ancestralCauchy

  object are plotted.

• n_col: the number of columns on which to display the plot. Can be missing, in which case a default number is used.

• intervals: a list of HDI intervals produced by function hdi.ancestralCauchy. If the HDI of a plotted node is in the list, then it is plotted by the function.

• ...: further arguments to be passed to plot.

Returns

None.

Examples

set.seed(1289)
# Simulate tree and data
phy <- ape::rphylo(10, 0.1, 0)
dat <- rTraitCauchy(n = 1, phy = phy, model = "cauchy",
                    parameters = list(root.value = 10, disp = 0.1))
# Fit the data
fit <- fitCauchy(phy, dat, model = "cauchy", method = "reml")
# Reconstruct the ancestral values
inc <- increment(fit, node = c(3, 8), values = seq(-3, 3, 0.01))
plot(inc, type = "l")
anc <- ancestral(fit, node = c(12, 17), n_values = 1000)
plot(anc, type = "l")

See Also

plot_asr, ancestral, increment, fitCauchy