getSkylines - 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)

Value¶

Bayesian Skyline values for given clone

Details¶

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