fast.geomorph.phylo.integration: Fast covariance-based implementations of distance-based...
In phylocurve: Phylogenetic Comparative Methods for High-Dimensional Traits

Description Usage Arguments Details Value Author(s) References See Also Examples

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.

1 2	fast.geomorph.phylo.integration(A1, A2, phy, iter = 1000, label = NULL, verbose = FALSE, ShowPlot = TRUE)

`A1`	From geomorph: A 2D array (n x [p1 x k1]) or 3D array (p1 x k1 x n) containing landmark coordinates for the first block
`A2`	From geomorph: A 2D array (n x [p2 x k2]) or 3D array (p2 x k2 x n) containing landmark coordinates for the second block
`phy`	From geomorph: A phylogenetic tree of class phylo
`iter`	From geomorph: Number of iterations for significance testing
`label`	From geomorph: An optional vector indicating labels for each specimen that are to be displayed
`verbose`	From geomorph: A logical value indicating whether the output is basic or verbose
`ShowPlot`	From geomorph: A logical value indicating whether or not the plot should be returned

See phylo.integration

Eric W. Goolsby

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. and R. Felice. 2014. Assessing phylogenetic morphological integration and trait covariation in morphometric data using evolutionary covariance matrices. PLOS ONE. 9(4):e94335.

phylo.integration

### 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

# NOTE: phylo.integration is phylo.integration in newer versions of geomorph
# phylo.integration(Y.gpa$coords[1:5,,],Y.gpa$coords[6:11,,],plethspecies$phy,iter=99)
# phylo.integration(Y.gpa$coords[1:5,,],Y.gpa$coords[6:11,,],plethspecies$phy,iter=99)
fast.geomorph.phylo.integration(Y.gpa$coords[1:5,,],Y.gpa$coords[6:11,,],plethspecies$phy)