pml.fit: Internal maximum likelihood functions.

In phangorn: Phylogenetic Reconstruction and Analysis

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")

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".

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 [e-mail]

References

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

See Also

pml, pml_bb, pmlPart, pmlMix

Examples

data(Laurasiatherian)
tree <- NJ(dist.ml(Laurasiatherian))
bf <- rep(0.25, 4)
eig <- edQt()
pml.init(Laurasiatherian)
pml.fit(tree, Laurasiatherian, bf=bf, eig=eig)
pml.free()
pml(tree, Laurasiatherian) |> logLik()

phangorn documentation built on Sept. 17, 2024, 5:08 p.m.