pml.control: Auxiliary for Controlling Fitting
In KlausVigo/phangorn: Phylogenetic Reconstruction and Analysis

pml.control

R Documentation

Auxiliary for Controlling Fitting

Description

Auxiliary functions for providing optim.pml, pml_bb fitting. Use it to construct a control or ratchet.par argument.

Usage

pml.control(epsilon = 1e-08, maxit = 10, trace = 1, tau = 1e-08,
  statefreq = "empirical")

ratchet.control(iter = 20L, maxit = 200L, minit = 100L, prop = 1/2,
  rell = TRUE, bs = 1000L)

Arguments

`epsilon`	Stop criterion for optimization (see details).
`maxit`	Maximum number of iterations (see details).
`trace`	Show output during optimization (see details).
`tau`	minimal edge length.
`statefreq`	take "empirical" or "estimate" state frequencies.
`iter`	Number of iterations to stop if there is no change.
`minit`	Minimum number of iterations.
`prop`	Only used if `rearrangement=stochastic`. How many NNI moves should be added to the tree in proportion of the number of taxa.´
`rell`	logical, if TRUE approximate bootstraping similar Minh et al. (2013) is performed.
`bs`	number of approximate bootstrap samples.

Details

pml.control controls the fitting process. epsilon and maxit are only defined for the most outer loop, this affects pmlCluster, pmlPart and pmlMix.

epsilon is not an absolute difference between, but instead is defined as (logLik(k)-logLik(k+1))/logLik(k+1). This seems to be a good compromise and to work reasonably well for small and large trees or alignments.

If trace is set to zero than no out put is shown, if functions are called internally than the trace is decreased by one, so a higher of trace produces more feedback. It can be useful to figure out how long an run will take and for debugging.

statefreq controls if base/state frequencies are optimized or empirical estimates are taken, when this applies. For some nucleotide models (e.g. JC, SYM) equal base frequencies and for amino acid models precomputed state frequencies are used, if not '+F' is specified.

tau might be exactly zero if duplicated sequences in the alignment are observed. In this case the analysis is performed only on unique sequences and duplicated taxa are added to the tree with zero edge length. This may lead to multifurcations if there are three or more identical sequences. After optimization it is good practice to prune away edges of length tau using di2multi. See also Janzen et al. (2021).

Value

A list with components named as the arguments for controlling the fitting process.

Author(s)

Klaus Schliep klaus.schliep@gmail.com

References

Minh, B. Q., Nguyen, M. A. T., & von Haeseler, A. (2013). Ultrafast approximation for phylogenetic bootstrap. Molecular biology and evolution, 30(5), 1188-1195.

Janzen, T., Bokma, F.,Etienne, R. S. (2021) Nucleotide Substitutions during Speciation may Explain Substitution Rate Variation, Systematic Biology, 71(5), 1244–1254.