Description Usage Arguments Value Author(s) See Also Examples
smaller.clade.spectrum
returns a n*2 matrix where n is the number of internal nodes of the tree. For each i in 1:n, the [i,1] element of the matrix is the size of the clade rooted at the 'i'th node of the tree. [i,2] is the size of the smaller daughter clade of the 'i'th node of the tree.
1 | smaller.clade.spectrum(tree)
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tree |
An object of class |
A n*2 matrix (where n is the number of internal nodes of the tree) containing the size of the clades and the smaller clades.
smaller.clade.spectrum(tree)[1,1]
contains the number of tips of the tree.
smaller.clade.spectrum(tree)[i,1]
contains the number of tips of the subtree whose root is the node number n-i+1
.
smaller.clade.spectrum(tree)[1,2]
contains the number of tips of the smaller daughter clade at the root.
Michael Blum <michael.blum@imag.fr>
Nicolas Bortolussi <nicolas.bortolussi@imag.fr>
Eric Durand <eric.durand@imag.fr>
Olivier Francois <olivier.franois@imag.fr>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | # computes the log-likelihood for Aldous' model
shape.new <- function(tree){
h <- function(n){sum(1/(1:n))}
mat <- smaller.clade.spectrum(tree)
parent <- mat[,1]
daughter <- mat[,2]
nh.n <- sapply(parent, FUN = function(x){x*h(x-1)} )
s <- sum(log(daughter/parent) + log(1 - daughter/parent) + log(nh.n))
return(s)}
# distribution over 200 replicates
tr <- rtreeshape(200, 100, FUN =
function(n,i){if((i>0)&(i<n))return(1/i/(n-i)) else return(0)})
res <- sapply( tr, FUN = shape.new)
hist(res)
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