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\name{rtt}
\alias{rtt}
\title{Root a Tree by Root-to-Tip Regression}
\description{
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$double.eps^0.25)
}
\arguments{
\item{t}{an object of class \code{"phylo"}.}
\item{tip.dates}{a vector of sampling times associated to the tips of
\code{t}, in the same order as \code{t$tip.label}.}
\item{ncpu}{number of cores to use.}
\item{objective}{one of \code{"correlation"}, \code{"rms"}, or
\code{"rsquared"}.}
\item{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.
\code{t} must have branch lengths in units of expected substitutions
per site.
\code{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 \code{ncpu} to a value larger than 1 requires the \code{parallel}
library.
\code{objective} is the measure which will be used to define the
``goodness'' of a regression fit. It may be one of \code{"correlation"}
(strongest correlation between tip date and distance from root),
\code{"rms"} (lowest root-mean-squared error), or \code{"rsquared"}
(highest R-squared value).
\code{opt.tol} is used to optimize the location of the root along the best
branch. By default, R's \code{optimize} function uses a precision of
\code{.Machine$double.eps^0.25}, which is about 0.0001 on a 64-bit system.
This should be set to a smaller value if the branch lengths of \code{t} are
very short.
}
\value{
an object of class \code{"phylo"}.
}
\note{
This function only chooses the best root. It does not rescale the branch
lengths to time, or perform a statistical test of the molecular clock
hypothesis.
}
\author{
Rosemary McCloskey\email{rmccloskey@cfenet.ubc.ca},
Emmanuel Paradis
}
\references{
Rambaut, A. (2009). Path-O-Gen: temporal signal investigation
tool.
Rambaut, A. (2000). Estimating the rate of molecular evolution:
incorporating non-contemporaneous sequences into maximum likelihood
phylogenies. \emph{Bioinformatics}, \bold{16}, 395-399.
}
\examples{
t <- rtree(100)
tip.date <- rnorm(t$tip.label)^2
rtt(t, tip.date)
}
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