#### added the Rtreemix package and removed the bim package

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rtreemix@28790 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 16/11/2007 21:25:16
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 1 1 new file mode 100644 ... ... @@ -0,0 +1,54 @@ 1 +\name{comp.trees}  2 +  3 +\alias{comp.trees}  4 +\alias{comp.trees.levels}  5 +  6 +\title{Functions for quantifying the diversity of the nontrivial trees in  7 +a mutagenetic trees mixture model}  8 +\description{  9 + These functions implement a similarity measure for comparing the topologies  10 + of the nontrivial tree components of a specified mixture  11 + model, and thereby quantifying their diversity.  12 + All possible pairs of nontrivial components are considered when  13 + computing the similarity. \code{comp.trees} uses the sum of the number of  14 + different edges of all pairs for caracterizing  15 + the difference of the trees in the model. \code{comp.trees.levels} uses  16 + the sum of the number of different edges of all pairs and the  17 + corresponding L1 distances of their level vectors. The model must have at  18 + least two nontrivial components.  19 +}  20 +\usage{  21 +comp.trees(model)  22 +comp.trees.levels(model)  23 +}  24 +  25 +\arguments{  26 + \item{model}{An \code{RtreemixModel} object.}  27 +}  28 +  29 +\value{  30 + The functions return a numeric value that quantifies the similarity  31 + (or diversity) of the nontrivial tree topologies of a given mixture models.  32 +}  33 +  34 +\author{Jasmina Bogojeska}  35 +  36 +\seealso{  37 + \code{\link{RtreemixModel-class}}, \code{\link{comp.models}},  38 + \code{\link{fit-methods}}, \code{\link{stability.sim}}  39 +}  40 +  41 +\examples{  42 +## Generate two random RtreemixModel objects each with 3 components.  43 +mix1 <- generate(K = 3, no.events = 9, noise.tree = TRUE, prob = c(0.2, 0.8))  44 +mix2 <- generate(K = 3, no.events = 9, noise.tree = TRUE, prob = c(0.2, 0.8))  45 +## Inspect the diversity of the nontrivial tree components in a given model  46 +## using the number of distinct edges and the levels of the events in  47 +## the treesas dissimilarity measure.  48 +comp.trees.levels(model = mix1)  49 +comp.trees.levels(model = mix2)  50 +}  51 +  52 +  53 +\keyword{misc}  54 +