# rtt

##### Root a Tree by Root-to-Tip Regression

This function roots a phylogenetic tree with dated tips in the location most compatible with the assumption of a strict molecular clock.

##### Usage

```
rtt(t, tip.dates, ncpu = 1, objective = correlation,
opt.tol = .Machine$double.eps^0.25)
```

##### Arguments

- t
an object of class

`"phylo"`

.- tip.dates
a vector of sampling times associated to the tips of

`t`

, in the same order as`t$tip.label`

.- ncpu
number of cores to use.

- objective
one of

`"correlation"`

,`"rms"`

, or`"rsquared"`

.- opt.tol
tolerance for optimization precision.

##### Details

This function duplicates one part the functionality of the program Path-O-Gen (see references). The root position is chosen to produce the best linear regression of root-to-tip distances against sampling times.

`t`

must have branch lengths in units of expected substitutions
per site.

`tip.dates`

should be a vector of sampling times, in any time
unit, with time increasing toward the present. For example, this may
be in units of ``days since study start'' or ``years since 10,000
BCE'', but not ``millions of yearsago''.

Setting `ncpu`

to a value larger than 1 requires the `parallel`

library.

`objective`

is the measure which will be used to define the
``goodness'' of a regression fit. It may be one of `"correlation"`

(strongest correlation between tip date and distance from root),
`"rms"`

(lowest root-mean-squared error), or `"rsquared"`

(highest R-squared value).

`opt.tol`

is used to optimize the location of the root along the best
branch. By default, R's `optimize`

function uses a precision of
`.Machine$double.eps^0.25`

, which is about 0.0001 on a 64-bit system.
This should be set to a smaller value if the branch lengths of `t`

are
very short.

##### Value

an object of class `"phylo"`

.

##### Note

This function only chooses the best root. It does not rescale the branch lengths to time, or perform a statistical test of the molecular clock hypothesis.

##### References

Rambaut, A. (2009). Path-O-Gen: temporal signal investigation tool. http://tree.bio.ed.ac.uk/software/pathogen/

Rambaut, A. (2000). Estimating the rate of molecular evolution:
incorporating non-contemporaneous sequences into maximum likelihood
phylogenies. *Bioinformatics*, **16**, 395-399.

##### Examples

```
# NOT RUN {
t <- rtree(100)
tip.date <- rnorm(t$tip.label)^2
rtt(t, tip.date)
# }
```

*Documentation reproduced from package ape, version 4.1, License: GPL (>= 2)*