tree_reorder: Reorder tree tips to best match a desired order
In bnpsd: Simulate Genotypes from the BN-PSD Admixture Model

Description Usage Arguments Details Value See Also Examples

This functions reorganizes the tree structure so that its tips appear in a desired order if possible, or in a reasonably close order when an exact solution is impossible. This tip order in the output tree is the same in both the tip labels vector (tree$tip.label) and edge matrix (tree$edge), ensured by using tree_reindex_tips() internally.

1	tree_reorder(tree, labels)

`tree`	A `phylo` object from the `ape` package (see `ape::read.tree()`). Works with standard `phylo` objects, and also with our extended trees (in that additive edges `tree$edge.length.add` are recalculated after reordering if they were present).
`labels`	A character vector with all tip labels in the desired order. Must contain each tip label in `tree` exactly once.

This function has the same goal as ape::rotateConstr(), which implements a different heuristic algorithm that did not perform well in our experience.

The modified tree (phylo object) with reordered edges and tips.

tree_reindex_tips() to reorder tips in the labels vector to match the edge matrix order, which ensures agreement in plots (assuming plot show desired order already).

# create a random tree
library(ape)
k <- 5
tree <- rtree( k )
# let's set the current labels as the desired order
labels <- tree$tip.label

# now let's scramble the edges on purpose
# to create an example where reordering is needed

tree_rand <- tree
# new order of edges
indexes <- sample( Nedge( tree_rand ) )
# reorder all edge values
tree_rand$edge <- tree_rand$edge[ indexes, ]
tree_rand$edge.length <- tree_rand$edge.length[ indexes ]
# now let's reorder edges slightly so tree is more reasonable-looking
# (otherwise plot looks tangled)
tree_rand <- reorder( tree_rand, order = 'postorder' )
# the order of the tip labels in the vector and on the plot disagree with each other:
tree_rand$tip.label
plot( tree_rand )

# now reorder tree object so tips are in the desired order:
tree_rand <- tree_reorder( tree_rand, labels )
# now tip labels vector and plot should agree in order:
# (the original tree was recovered!)
tree_rand$tip.label
plot( tree_rand )

# order the tree in a different way than the original order
labels <- paste0( 't', 1 : k )
# in this case, it's often impossible to get a perfect output order
# (because the tree structure constrains the possible plot orders),
# but this function tries its best to get close to the desired order
tree2 <- tree_reorder( tree, labels )
plot(tree2)