Drop tips from a phylogenetic tree by their state values

drop_tips_by_state() will remove from a phylo object all tips in a specified state(s).

Usage

drop_tips_by_state(tree, drop_values)

Arguments

tree

An object of class phylo with a tip.state attribute. See add_tip_states() for adding tip annotations to a phylo object.

drop_values

Character vector of states to remove.

Value

An object of class phylo with the specified states removed.

See also

add_tip_states() to add tip annotations

Examples

# This demo tree has 13 tips in 3 possible states
demo_tree_prepared
#> 
#> Phylogenetic tree with 13 tips and 12 internal nodes.
#> 
#> Tip labels:
#>   sp2, sp4, sp8, sp9, sp10, sp26, ...
#> Node labels:
#>   nd1, nd2, nd6, nd22, nd27, nd74, ...
#> 
#> Rooted; includes branch length(s).
table(demo_tree_prepared$tip.state)
#> 
#> 1 2 3 
#> 2 6 5 

# Remove all tips in state 3
new_tree <- drop_tips_by_state(demo_tree_prepared, "3")

# The resulting tree has 8 tips, having removed all tips in state 3
new_tree
#> 
#> Phylogenetic tree with 8 tips and 7 internal nodes.
#> 
#> Tip labels:
#>   sp2, sp4, sp8, sp9, sp26, sp30, ...
#> Node labels:
#>   nd1, nd2, nd6, nd22, nd27, nd32, ...
#> 
#> Rooted; includes branch length(s).
table(new_tree$tip.state)
#> 
#> 1 2 
#> 2 6