X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=man%2Frtree.Rd;fp=man%2Frtree.Rd;h=514f39bbdbf1ec9a50c73329fb178d1c96b9ec00;hb=199144b0297c3fc76d76c29e561151235e39f0af;hp=b30109cdcbf86eafcd99942067edb0ab04f497fb;hpb=bb212c8b0bb52b72923c0e9a6ec942b81c681a38;p=ape.git diff --git a/man/rtree.Rd b/man/rtree.Rd index b30109c..514f39b 100644 --- a/man/rtree.Rd +++ b/man/rtree.Rd @@ -3,6 +3,12 @@ \alias{rcoal} \alias{rmtree} \title{Generates Random Trees} +\description{ + These functions generate trees by splitting randomly the edges + (\code{rtree}) or randomly clustering the tips (\code{rcoal}). + \code{rtree} generates general trees, and \code{rcoal} generates + coalescent trees. The algorithms are described in Paradis (2012). +} \usage{ rtree(n, rooted = TRUE, tip.label = NULL, br = runif, ...) rcoal(n, tip.label = NULL, br = "coalescent", ...) @@ -23,12 +29,6 @@ rmtree(N, n, rooted = TRUE, tip.label = NULL, br = runif, ...) \item{\dots}{further argument(s) to be passed to \code{br}.} \item{N}{an integer giving the number of trees to generate.} } -\description{ - These functions generate trees by splitting randomly the edges - (\code{rtree}) or randomly clustering the tips (\code{rcoal}). - \code{rtree} generates general (non-ultrametric) trees, and - \code{rcoal} generates coalescent (ultrametric) trees. -} \details{ The trees generated are bifurcating. If \code{rooted = FALSE} in (\code{rtree}), the tree is trifurcating at its root. @@ -44,6 +44,10 @@ rmtree(N, n, rooted = TRUE, tip.label = NULL, br = runif, ...) An object of class \code{"phylo"} or of class \code{"multiPhylo"} in the case of \code{rmtree}. } +\references{ + Paradis, E. (2012) \emph{Analysis of Phylogenetics and Evolution with + R (Second Edition).} New York: Springer. +} \author{Emmanuel Paradis} \seealso{ \code{\link{stree}}, \code{\link{rlineage}}