estimate_band_W {ontophylo}

Estimate bandwidth

Description

Estimate the bandwidth for the Markov KDE.

Usage

estimate_band_W(
  tree.discr,
  data.path,
  band.width = c("bw.nrd0", "bw.nrd0", "bw.ucv", "bw.bcv", "bw.SJ")
)

Arguments

tree.discr

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

data.path

list. A list of path data obtained from the 'make_data_NHPP_KDE_Markov_kernel' function.

band.width

character. Bandwidth selectors for the KDE, as in density.

Value

A numeric vector.

Author(s)

Sergei Tarasov

Examples

data("hym_hm", "hym_tree")
# Get reference tree.
tree_discr <- discr_Simmap(hym_tree, res = 200)
# Get hamming data from the head characters.
hm <- hym_hm$head
# Make NHPP path data.
nhpp_psd <- make_data_NHPP_KDE_Markov_kernel(hm, add.psd = TRUE)
# Calculate bandwidth.
bdw <- estimate_band_W(tree_discr, nhpp_psd, band.width = "bw.nrd0")
mean(bdw)