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Reformat a phylogenetic tree to be compatible with saasi

Source: R/prepare_tree_for_saasi.R
prepare_tree_for_saasi.Rd

prepare_tree_for_saasi() will take in a phylo object and reformat it so that the output is compabtible with the saasi function. This reformatting includes:

  • Adding tip annotations

  • Resolving polytomies

  • Imposing a minimum branch length

  • Removing undesired states

Usage

prepare_tree_for_saasi(
  tree,
  tip_data = NULL,
  resolve_polytomies = TRUE,
  fix_branches = TRUE,
  min_branch_length = 1e-05,
  drop_states = character(0)
)

Arguments

tree

An object of class phylo.

tip_data

Either a named vector or a data.frame. If a named vector, the elements of the vector must be the state of each tip and the names must be the labels of those tips. If a data.frame, there must be 2 columns: the first with the tip labels and the second with the tip states. This can be omitted if tree already has a tip.states attribute.

resolve_polytomies

Boolean. Indicates whether polytomies should be resolved. Default value is TRUE. Setting to FALSE will produce a tree that is incompatible with saasi.

fix_branches

Boolean. Indicates whether zero and negative branch lengths should be fixed. Default value is TRUE. Setting to FALSE will produce a tree that is incompatible with saasi.

min_branch_length

Numeric. The minimum branch length for the resultant tree. Any short branch lengths will be increased accordingly. Default value is 1e-5.

drop_states

An optional character vector of states to remove from the tree.

Value

An object of class phylo that is compatible with the saasi() function.

Details

The reformatting is conducted as follows:

  • Polytomies are resolved using ape::multi2di().

  • The length of any branches with zero or negative length is set to min_branch_length.

  • All tips with an NA value for their state annotation are removed in addition to any states specified in drop_states.

See also

add_tip_states() to manually add state annotations to tip states or drop_tips_by_state() to manually remove tips from the tree based on their state.

Examples

# Check if the demo tree is compatible
check_tree_compatibility(demo_tree)
#> Tree is not compatible with SAASI
#> NA tip states present. Remove with drop_tips_by_state(tree, NA)
#> No tip states. Attach with attach_tip_states() or prepare_tree_for_saasi()
#> [1] FALSE

# Since tip annotations are missing, we need state data for the tips
head(demo_metadata)
#>   node state
#> 1  sp2     1
#> 2  sp4     2
#> 3  sp8     2
#> 4  sp9     1
#> 5 sp10     3
#> 6 sp26     2

# Reformat the demo tree with the tip states
tree_prepared <- prepare_tree_for_saasi(demo_tree, demo_metadata)

# Check the compability of the reformatted tree
check_tree_compatibility(tree_prepared)
#> Tree is compatible with SAASI
#> [1] TRUE