R: Internal maximum likelihood functions.

discrete.gamma {phangorn} | R Documentation

## Internal maximum likelihood functions.

### Description

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

### Usage

    discrete.gamma(alpha, k)

    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

`alpha` | Shape parameter of the gamma distribution.
`k` | Number of intervals of the discrete gamma distribution.
`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.
`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.

### 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.

### See Also

`pml, pmlPart, pmlMix`

[Package phangorn version 2.3.1 Index]