fast.geomorph.compare.multi.evol.rates: 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.compare.multi.evol.rates(A, gp,
phy, Subset = TRUE, method = "ML", ShowPlot = TRUE, iter = 1000)

Arguments

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
gp	From geomorph: A factor array designating group membership
phy	From geomorph: A phylogenetic tree of class phylo
Subset	From geomorph: A logical value indicating whether or not the traits are subsets from a single landmark configuration (default is TRUE)
method	Maximum likelihood "ML" or restricted maximum likelihood "REML"
ShowPlot	From geomorph: A logical value indicating whether or not the plot should be returned
iter	From geomorph: Number of iterations for significance testing

Details

See compare.multi.evol.rates

Value

See compare.multi.evol.rates

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.

Adams, D.C. 2014. Quantifying and comparing phylogenetic evolutionary rates for shape and other high-dimensional phenotypic data. Syst. Biol. 63:166-177.

Denton, J.S.S., and D.C. Adams. 2015. A new phylogenetic test for comparing multiple high-dimensional evolutionary rates suggests interplay of evolutionary rates and modularity in lanternfishes (Myctophiformes; Myctophidae). Evolution. 69: doi:10.1111/evo.12743

See Also

compare.multi.evol.rates

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
land.gp<-c("A","A","A","A","A","B","B","B","B","B","B")  #mandible and cranium subsets

compare.multi.evol.rates(Y.gpa$coords,land.gp,phy=plethspecies$phy,iter=99)
fast.geomorph.compare.multi.evol.rates(Y.gpa$coords,land.gp,plethspecies$phy)

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