pml.control: 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)

Value

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

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.

Author

Klaus Schliep klaus.schliep@gmail.com

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.

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.

Examples

Run this code

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

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