| roottotip {BactDating} | R Documentation |
Root to tip correlation
roottotip(tree, date, rate = NA, permTest = 10000, showFig = T, colored = T, showPredInt = "gamma", showText = T, showTree = T)
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 |
List containing estimated clock rate, date of origin and p-value