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

In ericgoolsby/phylocurve: Phylogenetic Comparative Methods for High-Dimensional Traits

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

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

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)

ericgoolsby/phylocurve documentation built on April 28, 2021, 10:23 p.m.