phylocurve (version 2.1.1)

fast.geomorph.compare.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.evol.rates(phy, A, gp,
method = "ML", ShowPlot = TRUE, iter = 1000,
censored = FALSE, force.diag = FALSE)

Arguments

phy

An object 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

gp

From geomorph: A factor array designating group membership

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

censored

Whether or not to use the censored approach for estimating regime-specific evolutionary rates (O'Meara et al. 2006). The censored approach is more efficient and has identical statistical power to the default method based on phylogenetic transformation of residuals.

force.diag

Whether or not to assume trait independence (a diagonal evolutionary rate matrix), as was originally described in Adams (2014c) and implemented in geomorph up to version 2.1.5. Should normally be set to FALSE (the default) unless trait independence is deliberately assumed.

Value

See compare.evol.rates

Details

See compare.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.

See Also

compare.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

 gp.end<-factor(c(0,0,1,0,0,1,1,0,0))  #endangered species vs. rest
 names(gp.end)<-plethspecies$phy$tip

#Calculate rates of shape
compare.evol.rates(phy=plethspecies$phy,Y.gpa$coords,gp=gp.end,iter=49)
fast.geomorph.compare.evol.rates(plethspecies$phy,Y.gpa$coords,gp=gp.end)

#Calculate rates of size
compare.evol.rates(phy=plethspecies$phy,Y.gpa$Csize,gp=gp.end,iter=49)
fast.geomorph.compare.evol.rates(plethspecies$phy,Y.gpa$Csize,gp=gp.end,iter=49)
# }