calcOvrlp: Calculate phylogenetic overlap

In treeman: Phylogenetic Tree Manipulation Class and Methods

Description

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.

See Also

calcPhyDv https://github.com/DomBennett/treeman/wiki/calc-methods

Examples

library(treeman)
tree <- randTree(10)
ids_1 <- sample(tree['tips'], 5)
ids_2 <- sample(tree['tips'], 5)
calcOvrlp(tree, ids_1, ids_2)

treeman documentation built on July 8, 2020, 7:28 p.m.