Skip to contents

Check if phylogenetic tree is compatible with saasi

Source: R/check_tree_compatibility.R
check_tree_compatibility.Rd

Verifies the compatibility of a phylo object with the saasi() function without modifying the object. For tree to be compatible with saasi(), it must:

  • be rooted,

  • have the correct number of internal nodes (the number of tips - 1),

  • have no unary nodes or polytomies,

  • have positive branch lengths, and

  • have valid tip state annotations for all tips.

If the tree is not compatible with saasi(), the user can run prepare_tree_for_saasi() to resolve the issues.

Usage

check_tree_compatibility(tree)

Arguments

tree

An object of class phylo.

Value

Logical. Returns TRUE if the tree is compatible with saasi and FALSE otherwise.

Examples

# Check if this demo tree is compatible with saasi:
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

# Now check another tree which has been properly prepared:
check_tree_compatibility(demo_tree_prepared)
#> Tree is compatible with SAASI
#> [1] TRUE