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

Arguments

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

Details

See phylo.integration

Value

See phylo.integration

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

See Also

phylo.integration

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

# 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)

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