phangorn: pml.fit – R documentation

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phangorn

pml.fit

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

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
`Mkv`	indicate if Lewis' Mkv should be estimated.
`site.rate`	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.

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.

Value

pml.fit returns the log-likelihood.

Author(s)

Klaus Schliep klaus.schliep@gmail.com

References

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