test_mast.R
In phangorn: Phylogenetic Reconstruction and Analysis

## generate data
set.seed(42)
tree1 <- rtree(100)
tree2 <- rSPR(tree1, 5)
tips <- mast(tree1, tree2, tree = FALSE)
mast_tree <- mast(tree1, tree2)

tip_label <- tree1$tip.label

tips_to_delete <- setdiff(tip_label, tips)

tree1_drop <- drop.tip(tree1, tips_to_delete)
tree2_drop <- drop.tip(tree2, tips_to_delete)


# test maximum agreement subtree (MAST)
## common subtrees should be identical
expect_equal(RF.dist(tree1_drop, tree2_drop), 0)
expect_equal(RF.dist(tree1_drop, mast_tree), 0)
expect_equal(RF.dist(tree2_drop, mast_tree), 0)