fast.geomorph.physignal: DEPRECATED: Fast covariance-based implementations of...

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

Description

All fast.geomorph functions are deprecated and will be removed from phylocurve soon. If you are trying to perform distanced-based phylogenetic comparative methods on high-dimensional data, please use and cite the geomorph package.

The functions fast.geomorph.compare.evol.rates, fast.geomorph.compare.multi.evol.rates, fast.geomorph.phylo.integration, fast.geomorph.procD.pgls , and fast.geomorph.physignal are covariance-baesd implementations of the geomorph functions compare.evol.rates, compare.multi.evol.rates, phylo.integration, 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

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

### 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")

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