shiftNodeAge: Modify Node Ages in Ultramtric Trees
In fmichonneau/phyloch: Tools for phylogenetics and taxonomy

Description Usage Arguments Value Author(s) See Also Examples

The functions is intended to manually change the height of internal nodes (i.e. changing the 'age of nodes'), e.g. to create a tree prior for Bayesian phylogeny estimation (BEAST, etc.).

1	shiftNodeAge(phy, node, shift = NULL, age = NULL)

`phy`	An object of class `"phylo"`. Must be ultrametric (see `is.ultrametric`)
`node`	An integer, the number of the internal node whose age is to be modified.
`shift`	A real number giving the age shift of `node` in the same units as the branch lengths od `phy`. Positive numbers shift the node back in time; negative numbers render it younger. `shift` is overridden by `age`.
`age`	A real number giving the new age of `node` in the same units as the branch lengths of `phy`. Overrides `shift`.

An object of class "phylo"

Christoph Heibl

rbeauti, compare.phylo

# Phylogeny of bird orders:
data(bird.orders)

# Have a look at the phylogeny:
plot(bird.orders)
axisPhylo()

# Change age of node 42 ...
tr <- shiftNodeAge(bird.orders, 42, -15)

# ... plot again:
plot(tr)
axisPhylo()

# Alternatively, the result can be checked with 'compare.phylo':
compare.phylo(bird.orders, tr)

# Note that time shifts must not exceed the available 
# branch length:
#tr <- shiftNodeAge(bird.orders, 42, +15)