Returns the sum of branch lengths represented by ids_1 and ids_2 for a tree.
Usage
calcOvrlp(
tree,
ids_1,
ids_2,
nrmlsd = FALSE,
parallel = FALSE,
progress = "none"
)
Arguments
- tree
TreeMan object
- ids_1
tip ids of community 1
- ids_2
tip ids of community 2
- nrmlsd
Boolean, should returned value be between 0 and 1? Default, FALSE.
- parallel
logical, make parallel?
- progress
name of the progress bar to use, see create_progress_bar
Details
Use this to calculate the sum of branch lengths that are represented between two
communities. This measure is also known as the unique fraction. It can be used to measure
concepts of phylogenetic turnover. Parallelizable.
References
Lozupone, C., & Knight, R. (2005). UniFrac: a new phylogenetic method for comparing
microbial communities. Applied and Environmental Microbiology, 71(12), 8228-35.
Examples
tree <- randTree(10)
ids_1 <- sample(tree["tips"], 5)
ids_2 <- sample(tree["tips"], 5)
calcOvrlp(tree, ids_1, ids_2)
#> [1] 4.155736
