R: Calculate phylogenetic overlap

calcOvrlp {treeman} | R Documentation

## Calculate phylogenetic overlap

### 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)

[Package treeman version 1.1.4 Index]