pNHPP {ontophylo}

Phylogenetic Non-Homogeneous Poisson Process (pNHPP) method

Description

Wrapper function for applying the pNHPP method.

Usage

pNHPP(
  stm_amalg,
  tree = tree,
  res = res,
  add.psd = TRUE,
  band.width = c("bw.nrd0", "bw.nrd0", "bw.ucv", "bw.bcv", "bw.SJ"),
  lambda.post.stat = "Mean"
)

Arguments

stm_amalg

multiSimmap object. A list of amalgamated stochastic maps.

tree

simmap or phylo object. A reference tree for discretization.

res

integer. A resolution value for the discretization of tree edges.

add.psd

logical. Whether to add pseudodata or not in the 'make_data_NHPP_KDE_Markov_kernel' function. Default is TRUE.

band.width

character. Bandwidth selectors for the KDE in the 'estimate_band_W' function.

lambda.post.stat

character. A value with the statistic to be used in the 'make_postPois_KDE' function.

Value

A list with the estimated Markov KDE for all edges, the contMap object for plotting the NHPP, and the information necessary for making the edgeplot.

Author(s)

Diego Porto

Examples

  # Load data.
  data("hym_stm", "hym_stm_amalg")
  # Get a reference tree for discretization.
  tree <- hym_stm[[1]][[1]]
  # Get ten samples of stochastic maps from head.
  tree_list <- hym_stm_amalg$head[1:10]
  # Run the pNHPP method.
  nhpp_test <- pNHPP(tree_list, tree, res = 500,
  add.psd = TRUE, band.width = 'bw.nrd', lambda.post.stat = 'Mean')