phylocurve (version 2.1.1)

fast.geomorph.compare.multi.evol.rates: Fast covariance-based implementations of distance-based methods

Description

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

Value

See compare.multi.evol.rates

Details

See compare.multi.evol.rates

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

# NOT RUN {
### 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)
# }