K.mult: Test phylogenetic signal (Kmult) using phylogenetic...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/phylocurve.R

Description

An implementation of Kmult (Blomberg et al. 2003; Adams 2014) in which Kmult is compared to the null distribution generated by simulation on a star phylogeny (rather than phylogenetic permutation). Additionally, the expectation of the ratio of raw to phylogenetic mean squared error (the denominator of the formula for K) is estimated via phylogenetic simulation under Brownian motion.

Usage

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K.mult(model, nsim = 1000, plot = TRUE)

Arguments

model

An object of class evo.model.

nsim

The number of iterations for phylogenetic simulation.

plot

Whether or not to plot the null and alternative distribution of Kmult.

Value

An object of class compare.model.

Author(s)

Eric W. Goolsby

References

Golsby E.W. 2015. Likelihood-based parameter estimation for high-dimensional phylogenetic comparative models: overcoming the limitations of 'distance-based' methods. In review.

Adams D.C. 2014. A generalized K statistic for estimating phylogenetic signal from shape and other high-dimensional multivariate data. Syst. Biol. 63:685-697.

See Also

evo.model compare.models physignal

Examples

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rand.data <- sim.traits()
null.model <- evo.model(tree = rand.data$tree,
  Y = rand.data$trait_data,method = "Pairwise ML")

K.mult(model = null.model,nsim = 100)

Example output

sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 

Bootstrapping under null model.

**********Simulation results**********                                 
Test statistic (K)      1.7805348
Critical test statistic 0.4943335
Estimated Power         1.0000000

P-value: 0

phylocurve documentation built on Aug. 9, 2017, 9:03 a.m.