Description Usage Arguments Details Value Author(s) References See Also Examples
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.
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
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
1 2 3 4 5 6 7 8 9 10 11 12 13 | ### 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)
|
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