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,
  dir,
  id,
  time,
  burnin = 10,
  bins = 100,
  verbose = 0,
  forward = TRUE,
  nproc = 1,
  max_height = c("min", "median", "mean", "max")
)

Arguments

clones	clone tibble
dir	directory of BEAST trees file
id	unique identifer for this analysis
time	name of time column
burnin	Burnin percent (default 10)
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)

Details

Burnin set from readBEAST or getTrees

Value

Bayesian Skyline values for given clone

dowser documentation built on Nov. 5, 2025, 6:36 p.m.