lli: Internal maximum likelihood functions.

Description

These functions are internally used for the likelihood computations in pml or optim.pml.

Usage

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, ASC = FALSE, site.rate = "gamma")

Value

pml.fit returns the log-likelihood.

Arguments

data: An alignment, object of class phyDat.
tree: A phylogenetic tree, object of class phylo.
...: Further arguments passed to or from other methods.
Q: A vector containing the lower triangular part of the rate matrix.
bf: Base frequencies.
k: Number of intervals of the discrete gamma distribution.
shape: Shape parameter of the gamma distribution.
levels: The alphabet used e.g. c("a", "c", "g", "t") for DNA
inv: Proportion of invariable sites.
rate: Rate.
g: vector of quantiles (default is NULL)
w: vector of probabilities (default is NULL)
eig: Eigenvalue decomposition of Q
INV: Sparse representation of invariant sites
ll.0: default is NULL
llMix: default is NULL
wMix: default is NULL
site: return the log-likelihood or vector of sitewise likelihood values
ASC: ascertainment bias correction (ASC), allows to estimate models like Lewis' Mkv.
site.rate: Indicates what type of gamma distribution to use. Options are "gamma" approach of Yang 1994 (default), "gamma_quadrature" after the Laguerre quadrature approach of Felsenstein 2001 and "freerate".

Author

Klaus Schliep klaus.schliep@gmail.com

Details

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.

References

Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17, 368--376.