Fast covariance-based implementations of distance-based methods

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Description

The functions fast.geomorph.compare.evol.rates, fast.geomorph.compare.multi.evol.rates, fast.geomorph.phylo.pls, fast.geomorph.procD.pgls , and fast.geomorph.physignal are covariance-baesd implementations of the geomorph functions compare.evol.rates, compare.multi.evol.rates, phylo.pls, procD.pgls, and physignal using a fast linear-time algorithm. Code is directly modified from the original geomorph code for direct comparison between distance-based and covariance-based methods.

Usage

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fast.geomorph.physignal(phy, A, iter = 1000,
ShowPlot = TRUE, method = c("Kmult", "SSC"))

Arguments

phy

From geomorph: A phylogenetic tree of class phylo

A

From geomorph: A matrix (n x [p x k]) or 3D array (p x k x n) containing GPA-aligned coordinates for a set of specimens

iter

From geomorph: Number of iterations for significance testing

ShowPlot

From geomorph: A logical value indicating whether or not the plot should be returned

method

From geomorph: Method for estimating phylogenetic signal (Kmult or SSC)

Details

See physignal

Value

See physignal

Author(s)

Eric W. Goolsby

References

Goolsby E.W. 2016. Likelihood-Based Parameter Estimation for High-Dimensional Phylogenetic Comparative Models: Overcoming the Limitations of 'Distance-Based' Methods. In review.

Blomberg SP, Garland T, Ives AR. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution, 57:717-745.

Klingenberg, C. P., and N. A. Gidaszewski. 2010. Testing and quantifying phylogenetic signals and homoplasy in morphometric data. Syst. Biol. 59:245-261.

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

See Also

physignal

Examples

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### NOTE: this example is identical 
### to the example code for the
### analogous geomorph function
### for direct comparisons with
### 'fast.geomorph' phylocurve functions
require(geomorph)
data(plethspecies)
Y.gpa<-gpagen(plethspecies$land)    #GPA-alignment

#Test for phylogenetic signal in shape
physignal(phy=plethspecies$phy,Y.gpa$coords,iter=99)
fast.geomorph.physignal(plethspecies$phy,Y.gpa$coords,method="Kmult")

#Test for phylogenetic signal in size
physignal(phy=plethspecies$phy,Y.gpa$Csize,iter=99)
fast.geomorph.physignal(plethspecies$phy,Y.gpa$Csize,method="Kmult")

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