X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Fchronopl.Rd;h=6a5366c51524c43a7bd66ae4b788fbc94d58a12a;hb=6ee9e0a4e1e6bbc09187382bfdef57fafe3844c7;hp=fb2ddee2a6f07c5f491cf5ca3627a6fd61951d32;hpb=c827059eeafc8cbe41c812b26979543ab287803e;p=ape.git diff --git a/man/chronopl.Rd b/man/chronopl.Rd index fb2ddee..6a5366c 100644 --- a/man/chronopl.Rd +++ b/man/chronopl.Rd @@ -2,22 +2,36 @@ \alias{chronopl} \title{Molecular Dating With Penalized Likelihood} \usage{ -chronopl(phy, lambda, node.age = 1, node = "root", CV = FALSE) +chronopl(phy, lambda, age.min = 1, age.max = NULL, + node = "root", S = 1, tol = 1e-8, + CV = FALSE, eval.max = 500, iter.max = 500, ...) } \arguments{ \item{phy}{an object of class \code{"phylo"}.} - \item{lambda}{value of the smoothng parameter.} - \item{node.age}{numeric values specifying the fixed node ages.} + \item{lambda}{value of the smoothing parameter.} + \item{age.min}{numeric values specifying the fixed node ages (if + \code{age.max = NULL}) or the youngest bound of the nodes known to + be within an interval.} + \item{age.max}{numeric values specifying the oldest bound of the nodes + known to be within an interval.} \item{node}{the numbers of the nodes whose ages are given by - \code{node.age}; \code{"root"} is a short-cut the number of the - node.} + \code{age.min}; \code{"root"} is a short-cut for the root.} + \item{S}{the number of sites in the sequences; leave the default if + branch lengths are in mean number of substitutions.} + \item{tol}{the value below which branch lengths are considered + effectively zero.} \item{CV}{whether to perform cross-validation.} + \item{eval.max}{the maximal number of evaluations of the penalized + likelihood function.} + \item{iter.max}{the maximal number of iterations of the optimization + algorithm.} + \item{\dots}{further arguments passed to control \code{nlminb}.} } \description{ - This function estimates the node ages of a tree using semi-parametric - method based on penalized likelihood (Sanderson 2002). The branch - lengths of the input tree are interpreted as (mean) numbers of - substitutions. + This function estimates the node ages of a tree using a + semi-parametric method based on penalized likelihood (Sanderson + 2002). The branch lengths of the input tree are interpreted as mean + numbers of substitutions (i.e., per site). } \details{ The idea of this method is to use a trade-off between a parametric @@ -30,11 +44,26 @@ chronopl(phy, lambda, node.age = 1, node = "root", CV = FALSE) rate for all branches). \code{lambda} must be given. The known ages are given in - \code{node.age}, and the correponding node numbers in \code{node}. + \code{age.min}, and the correponding node numbers in \code{node}. These two arguments must obviously be of the same length. By default, an age of 1 is assumed for the root, and the ages of the other nodes are estimated. + If \code{age.max = NULL} (the default), it is assumed that + \code{age.min} gives exactly known ages. Otherwise, \code{age.max} and + \code{age.min} must be of the same length and give the intervals for + each node. Some node may be known exactly while the others are + known within some bounds: the values will be identical in both + arguments for the former (e.g., \code{age.min = c(10, 5), age.max = + c(10, 6), node = c(15, 18)} means that the age of node 15 is 10 + units of time, and the age of node 18 is between 5 and 6). + + The input tree may have multichotomies. If some internal branches are + of zero-length, they are collapsed (with a warning), and the returned + tree will have less nodes than the input one. The presence of + zero-lengthed terminal branches of results in an error since it makes + little sense to have zero-rate branches. + The cross-validation used here is different from the one proposed by Sanderson (2002). Here, each tip is dropped successively and the analysis is repeated with the reduced tree: the estimated dates for @@ -47,13 +76,19 @@ chronopl(phy, lambda, node.age = 1, node = "root", CV = FALSE) with the full phylogeny, \eqn{t_j^{-i}}{tj[-i]} is the estimated date for the \eqn{j}{j}th node after removing tip \eqn{i}{i} from the tree, and \eqn{n}{n} is the number of tips. + + The present version uses the \code{\link[stats]{nlminb}} to optimise + the penalized likelihood function: see its help page for details on + parameters controlling the optimisation procedure. } \value{ an object of class \code{"phylo"} with branch lengths as estimated by - the function. There are two or three further attributes: + the function. There are three or four further attributes: \item{ploglik}{the maximum penalized log-likelihood.} \item{rates}{the estimated rates for each branch.} + \item{message}{the message returned by \code{nlminb} indicating + whether the optimisation converged.} \item{D2}{the influence of each observation on overall date estimates (if \code{CV = TRUE}).} } @@ -63,9 +98,8 @@ chronopl(phy, lambda, node.age = 1, node = "root", CV = FALSE) approach. \emph{Molecular Biology and Evolution}, \bold{19}, 101--109. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ - \code{\link{chronogram}}, \code{\link{ratogram}}, - \code{\link{NPRS.criterion}}, \code{\link{chronoMPL}} + \code{\link{chronoMPL}} } \keyword{models}