make_contMap_KDE {ontophylo}

Make contMap KDE object

Description

Produces a contMap object for plotting the NHPP.

Usage

make_contMap_KDE(tree.discr, Edge.KDE.stat)

Arguments

tree.discr

phylo object. A discretized tree using the 'discr_Simmap' function.

Edge.KDE.stat

list. A list with the distributions of the estimated parameter of KDEs for each edge.

Value

A 'contMap' object.

Author(s)

Sergei Tarasov

Examples

data("hym_tree", "hym_kde")
# Get reference tree.
tree_discr <- discr_Simmap(hym_tree, res = 200)
# Get smoothing of normalized edge KDE data for mean rates.
Edge_KDE <- hym_kde$head
Edge_KDE_stat <- Edge_KDE$loess.lambda.mean
# Make contmap nhpp data.
nhpp_map <- make_contMap_KDE(tree_discr, Edge_KDE_stat)
# Plot contmap.
phytools::plot.contMap(nhpp_map, lwd = 3, outline = FALSE,
legend = FALSE, ftype = "off", plot = FALSE)