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Calculate phylogenetic overlap

Source: R/a.R
calcOvrlp.Rd

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


tree <- randTree(10)
ids_1 <- sample(tree["tips"], 5)
ids_2 <- sample(tree["tips"], 5)
calcOvrlp(tree, ids_1, ids_2)
#> [1] 4.155736