\name{comp.trees}
 
 \alias{comp.trees}
 \alias{comp.trees.levels}
 
 \title{Functions for quantifying the diversity of the nontrivial trees in
 a mutagenetic trees mixture model}
 \description{
  These functions implement a similarity measure for comparing the topologies
  of the nontrivial tree components of a specified mixture
  model, and thereby quantifying their diversity.
  All possible pairs of nontrivial components are considered when
  computing the similarity. \code{comp.trees} uses the sum of the number of
  different edges of all pairs for caracterizing
  the difference of the trees in the model. \code{comp.trees.levels} uses
  the sum of the number of different edges of all pairs and the
  corresponding L1 distances of their level vectors. The model must have at
  least two nontrivial components.
 }
 \usage{
 comp.trees(model)
 comp.trees.levels(model)
 }
 
 \arguments{
   \item{model}{An \code{RtreemixModel} object.}
 }
 
 \value{
   The functions return a numeric value that quantifies the similarity
   (or diversity) of the nontrivial tree topologies of a given mixture models.
 }
 
 \author{Jasmina Bogojeska}
  
 \seealso{
   \code{\link{RtreemixModel-class}}, \code{\link{comp.models}},
   \code{\link{fit-methods}}, \code{\link{stability.sim}}
 }
 
 \examples{
 ## Generate two random RtreemixModel objects each with 3 components.
 mix1 <- generate(K = 3, no.events = 9, noise.tree = TRUE, prob = c(0.2, 0.8))
 mix2 <- generate(K = 3, no.events = 9, noise.tree = TRUE, prob = c(0.2, 0.8))
 ## Inspect the diversity of the nontrivial tree components in a given model
 ## using the number of distinct edges and the levels of the events in
 ## the treesas dissimilarity measure.
 comp.trees.levels(model = mix1)
 comp.trees.levels(model = mix2)
 }
 
 
 \keyword{misc}