Usage
phyloFit(msa, tree=NULL, subst.mod="REV", init.mod=NULL,
no.freqs=FALSE, no.rates=FALSE, features=NULL, scale.only=FALSE,
scale.subtree=NULL, nrates=1, alpha=1, rate.constants=NULL,
init.random=FALSE, init.parsimony=FALSE, clock=FALSE, EM=FALSE,
precision="HIGH", ninf.sites=50, quiet=FALSE)Arguments
msa
An alignment object. May be altered if passed in as a pointer to
C memory (see Note).
tree
A character string containing a Newick formatted tree
defining the topology. Required if the number of species > 3, unles
init.mod is specified. The topology must be rooted, although the
root is ignored if the substitution model is reversible.
init.mod
An object of class tm used to initialize the model
no.freqs
(Only applies when init.mod provided). If TRUE, do
not estimate equilibrium frequencies; just use the ones from init.mod.
no.rates
(Only applies when init.mod provided). If TRUE,
do not estimate transition rate parameters; just use the transition
matrix in init.mod.
features
An object of type feat. If given, a separate model will be
estimated for each feature type.
scale.only
A logical value. If TRUE, estimate only the
scale of the tree. Branches will be held at initial values. Useful in
conjunction with init.mod.
scale.subtree
A character string giving the name of a node in
a tree. This option implies scale.only=TRUE. If given, estimate
separate scale factors for subtree beneath identified node and the rest
of the tree. The branch leading to the subtree is included in the su
nrates
An integer. The number of rate categories to use.
Specifying a value greater than one causes the discrete gamma model for
rate variation to be used, unless rate constants are specified.
alpha
A numeric value > 0, for use with "nrates". Initial value
for alpha, the shape parameter of the gamma distribution.
rate.constants
A numeric vector. Implies nrates =
length(rate.constants). Also implies EM=TRUE. Uses a non-parametric
mixture model for rates, instead of a gamma distribution. The weight
associated with each rate will be estimated. alpha may still be used to
initia
init.random
A logical value. If TRUE, parameters will be
initialized randomly.
init.parsimony
A logical value. If TRUE, branch lengths
will be estimated based on parsimony counts for the alignments.
Currently only works for models of order 0.
clock
A logical value. If TRUE, assume a molecular clock
in estimation.
EM
A logical value. If TRUE, the model is fit using EM
rather than the default BFGS quasi-Newton algorithm. Not available
for all models/options.
precision
A character vector, one of "HIGH", "MED", or "LOW",
denoting the level of precision to use in estimating model parameters.
Affects convergence criteria for iterative algorithms: higher precision
means more iterations and longer execution time.
ninf.sites
An integer. Require at least this many "informative"
sites in order to estimate a model. An informative site as an alignment
column with at least two non-gap and non-missing-data characers.
quiet
A logical value. If TRUE, do not report progress
to screen.