# lli

##### Internal maximum likelihood functions.

These functions are internally used for the likelihood computations in
`pml`

or `optim.pml`

.

- Keywords
- cluster

##### 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)

##### 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

##### 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.

##### References

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

##### See Also

*Documentation reproduced from package phangorn, version 2.5.5, License: GPL (>= 2)*