These functions are internally used for the likelihood computations in
pml or optim.pml.
lli(data, tree = NULL, ...)edQt(Q = c(1, 1, 1, 1, 1, 1), bf = c(0.25, 0.25, 0.25, 0.25))
pml.free()
pml.init(data, k = 1L)
pml.fit(tree, data, bf = rep(1/length(levels), length(levels)), shape = 1,
k = 1, Q = rep(1, length(levels) * (length(levels) - 1)/2),
levels = attr(data, "levels"), inv = 0, rate = 1, g = NULL,
w = NULL, eig = NULL, INV = NULL, ll.0 = NULL, llMix = NULL,
wMix = 0, ..., site = FALSE, Mkv = FALSE, site.rate = "gamma")
An alignment, object of class phyDat.
A phylogenetic tree, object of class phylo.
Further arguments passed to or from other methods.
A vector containing the lower triangular part of the rate matrix.
Base frequencies.
Number of intervals of the discrete gamma distribution.
Shape parameter of the gamma distribution.
The alphabet used e.g. c("a", "c", "g", "t") for DNA
Proportion of invariable sites.
Rate.
vector of quantiles (default is NULL)
vector of probabilities (default is NULL)
Eigenvalue decomposition of Q
Sparse representation of invariant sites
default is NULL
default is NULL
default is NULL
return the log-likelihood or vector of sitewise likelihood values
indicate if Lewis' Mkv should be estimated.
Indicates what type of gamma distribution to use. Options are "gamma" approach of Yang 1994 (default), "quadrature" after the Laguerre quadrature approach of Felsenstein 2001 and "freerate" .
pml.fit returns the log-likelihood.
These functions are exported to be used in different packages so far only in
the package coalescentMCMC, but are not intended for end user. Most of the
functions call C code and are far less forgiving if the import is not what
they expect than pml.
Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368--376.