Usage
phyloP.prior(mod, nsites=100, subtree=NULL, branches=NULL,
outfile=NULL, outfile.only=FALSE, quantiles=FALSE, epsilon=1e-10)Arguments
mod
An object of class tm representing the neutral model.
nsites
The number of sites in the alignment
subtree
Character string specifying the name of a node in the tree.
If given, partition the tree into the subtree beneath the node
and the complementary supertree, and compute joint number of substitutions
in the sub/supertree. The branch above the specified nod
branches
A vector of character strings givingi the names of
branches to consider in the subtree. The remaininig branches are
in the supertree. Return joint distribution of number of substitutions
in sub/supertree.
outfile
Character string. If given, write results to given file.
outfile.only
Logical. If TRUE, do not return any results
to R (this may be useful if results are very large).
quantiles
Logical. If TRUE, report quantiles of distribution
rather than whole distribution.
epsilon
Numeric value indicating the thhreshold used in truncating
tails of distributions; tail probabilities less than this value are
discarded. This only applies to the right tail.