dowser (version 2.5.1)

makeSkyline: get values for Bayesian Skyline plot

Description

makeSkyline

Usage

makeSkyline(
  object,
  bins = 100,
  youngest = 0,
  clone_id = NULL,
  max_height = c("min", "median", "mean", "max"),
  exclude_germline = TRUE
)

Value

Bayesian Skyline values for given clone

Arguments

object

treedata object with parameters_posterior and trees_posterior

bins

number of bins for plotting

youngest

timepoint of the most recently tip sampled (if 0, backward time used)

clone_id

name of the clone being analyzed (if desired)

max_height

max height to use (min, median, mean, max)

exclude_germline

exclude germline from skyline plot? (For TyCHE germline-rooted trees)