drop.tip method
drop.tip method
Usage
drop.tip(object, tip, ...)
drop.tip(object, tip, ...)
# S4 method for phylo
drop.tip(object, tip, ...)Source
drop.tip for phylo object is a wrapper method of ape::drop.tip from the ape package. The documentation you should read for the drop.tip function can be found here: drop.tip
Arguments
- object
A treedata or phylo object
- tip
a vector of mode numeric or character specifying the tips to delete
- ...
additional parameters
Author
Casey Dunn http://dunnlab.org and Guangchuang Yu https://guangchuangyu.github.io
Examples
nhxfile <- system.file("extdata/NHX", "ADH.nhx", package="treeio")
nhx <- read.nhx(nhxfile)
drop.tip(nhx, c("ADH2", "ADH1"))
#> 'treedata' S4 object that stored information
#> of
#> '/usr/lib/R/site-library/treeio/extdata/NHX/ADH.nhx'.
#>
#> [email protected] phylo:
#>
#> Phylogenetic tree with 4 tips and 3 internal nodes.
#>
#> Tip labels:
#> ADHY, ADHX, ADH4, ADH3
#>
#> Rooted; includes branch lengths.
#>
#> with the following features available:
#> 'B', 'D', 'S'.
#>
#> # The associated data tibble abstraction: 7 × 6
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#> node label isTip B D S
#> <int> <chr> <lgl> <dbl> <chr> <chr>
#> 1 1 ADHY TRUE NA NA nematode
#> 2 2 ADHX TRUE NA NA insect
#> 3 3 ADH4 TRUE NA NA yeast
#> 4 4 ADH3 TRUE NA NA yeast
#> 5 5 NA FALSE NA N NA
#> 6 6 NA FALSE NA N metazoa
#> 7 7 NA FALSE NA NA Fungi