pml.control: Auxiliary for Controlling Fitting

In phangorn: Phylogenetic Reconstruction and Analysis

Auxiliary for Controlling Fitting

Description

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

Usage

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

ratchet.control(iter = 20L, maxit = 200L, minit = 50L, 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.
iter	Number of iterations to stop if there is no change.
minit	Minimum number of iterations.
prop	Only used if rearrangement=stochstic. 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 defined as (logLik(k)-logLik(k+1))/logLik(k+1), this seems to be a good heuristics which works reasonably 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.

Value

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

Author(s)

Klaus Schliep [e-mail]

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.

See Also

optim.pml

Examples

pml.control()
pml.control(maxit=25)

phangorn documentation built on Jan. 23, 2023, 5:37 p.m.