getSkylines: Make data frames for Bayesian skyline plots

In dowser: B Cell Receptor Phylogenetics Toolkit

Make data frames for Bayesian skyline plots

Description

makeSkylines

Usage

getSkylines(
  clones,
  time,
  bins = 100,
  verbose = 0,
  forward = TRUE,
  nproc = 1,
  max_height = c("min", "median", "mean", "max"),
  exclude_germline = TRUE
)

Arguments

clones	clone tibble
time	name of time column
bins	number of bins for plotting
verbose	if 1, print name of clones
forward	plot in forward or (FALSE) backward time?
nproc	processors for parallelization (by clone)
max_height	max height to use (min, median, mean, max)
exclude_germline	exclude germline from skyline plot? (For TyCHE GRTs)

Details

Clones must contain treedata objects with parameters_posterior and trees_posterior. See readBEAST or getTimeTrees with posterior="all"

Value

Bayesian Skyline values for given clone

dowser documentation built on Aug. 20, 2026, 5:06 p.m.