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.procD.pgls(f1, phy, iter = 1000,
int.first = FALSE, verbose = FALSE)
|
f1 |
From geomorph: A formula for the linear model (e.g., y~x1+x2) |
phy |
From geomorph: A phylogenetic tree of class phylo |
iter |
From geomorph: Number of iterations for significance testing |
int.first |
From geomorph: A logical value to indicate if interactions of first main effects should precede subsequent main effects |
verbose |
From geomorph: A logical value specifying whether additional output should be displayed |
See procD.pgls
See procD.pgls
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. 2014. A method for assessing phylogenetic least squares models for shape and other high-dimensional multivariate data. Evolution. 68:2675-2688.
procD.pgls
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)
### Example of D-PGLS for high-dimensional data
data(plethspecies)
Y.gpa<-gpagen(plethspecies$land) #GPA-alignment
gdf <- geomorph.data.frame(Y.gpa, phy = plethspecies$phy)
procD.pgls(coords ~ Csize,data = gdf,plethspecies$phy,iter=1000)
fast.geomorph.procD.pgls(Y.gpa$coords ~ Y.gpa$Csize,plethspecies$phy)
|
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