modelTest {phangorn}

ModelTest

Description

Comparison of different nucleotide or amino acid substitution models

Usage

modelTest(object, tree = NULL, model = NULL, G = TRUE, I = TRUE,
  FREQ = FALSE, k = 4, control = pml.control(epsilon = 1e-08, maxit = 10,
  trace = 1), multicore = FALSE, mc.cores = NULL)

Arguments

object

an object of class phyDat or pml

tree

a phylogenetic tree.

model

a vector containing the substitution models to compare with each other or "all" to test all available models

G

logical, TRUE (default) if (discrete) Gamma model should be tested

I

logical, TRUE (default) if invariant sites should be tested

FREQ

logical, FALSE (default) if TRUE amino acid frequencies will be estimated.

k

number of rate classes

control

A list of parameters for controlling the fitting process.

multicore

logical, whether models should estimated in parallel.

mc.cores

The number of cores to use, i.e. at most how many child processes will be run simultaneously. Must be at least one, and parallelization requires at least two cores.

Details

modelTest estimates all the specified models for a given tree and data. When the mclapply is available, the computations are done in parallel. modelTest runs each model in one thread. This is may not work within a GUI interface and will not work under Windows.

Value

A data.frame containing the log-likelihood, number of estimated parameters, AIC, AICc and BIC all tested models. The data.frame has an attributes "env" which is an environment which contains all the trees, the data and the calls to allow get the estimated models, e.g. as a starting point for further analysis (see example).

Author(s)

Klaus Schliep [e-mail]

References

Burnham, K. P. and Anderson, D. R (2002) Model selection and multimodel inference: a practical information-theoretic approach. 2nd ed. Springer, New York

Posada, D. and Crandall, K.A. (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics 14(9): 817-818

Posada, D. (2008) jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25: 1253-1256

Darriba D., Taboada G.L., Doallo R and Posada D. (2011) ProtTest 3: fast selection of best-fit models of protein evolution. . Bioinformatics 27: 1164-1165

See Also

pml, anova, AIC, codonTest

Examples

## Not run: 
example(NJ)
(mT <- modelTest(Laurasiatherian, tree, model = c("JC", "F81", "K80", "HKY",
                 "SYM", "GTR")))

# extract best model
(best_model <- as.pml(mT))


data(chloroplast)
(mTAA <- modelTest(chloroplast, model=c("JTT", "WAG", "LG")))

# test all available amino acid models
(mTAA_all <- modelTest(chloroplast, model="all", multicore=TRUE, mc.cores=2))

## End(Not run)