fast.geomorph.compare.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.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.

Details

See compare.evol.rates

Value

See compare.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.

See Also

compare.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

 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)

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