roottotip: Root to tip correlation

In xavierdidelot/BactDating: BactDating: Bayesian inference of ancestral dates on bacterial phylogenetic trees

Root to tip correlation

Description

Root to tip correlation

Usage

roottotip(
  tree,
  date,
  rate = NA,
  permTest = 10000,
  showFig = T,
  colored = T,
  showPredInt = "gamma",
  showText = T,
  showTree = T
)

Arguments

tree	Phylogenetic tree
date	Dates of sampling
rate	Evolutionary rate, estimated unless provided
permTest	Number of permutations to perform to compute the p-value using a permutation test
showFig	Whether or not to show the root-to-tip regression figure
colored	Whether or not to use colors illustrating dates
showPredInt	To show 95percent confidence intervals of a strict clock model, can be 'poisson' or 'gamma'
showText	Whether to show the title and axis labels
showTree	Whether to show the tree or not

Value

List containing estimated clock rate, date of origin and p-value

xavierdidelot/BactDating documentation built on Oct. 21, 2024, 5:40 p.m.