Function quantifies the degree of phylogenetic morphological covariation between two or more sets of Procrustes-aligned coordinates using partial least squares.
phylo.integration(A, A2 = NULL, phy, partition.gp = NULL, iter = 999,
seed = NULL, print.progress = TRUE)
A 2D array (n x [p1 x k1]) or 3D array (p1 x k1 x n) containing landmark coordinates for the first block
An optional 2D array (n x [p2 x k2]) or 3D array (p2 x k2 x n) containing landmark coordinates for the second block
A phylogenetic tree of class phylo - see read.tree
in library ape
A list of which landmarks (or variables) belong in which partition (e.g. A,A,A,B,B,B,C,C,C) (required when only 1 dataset provided)
Number of iterations for significance testing
An optional argument for setting the seed for random permutations of the resampling procedure. If left NULL (the default), the exact same P-values will be found for repeated runs of the analysis (with the same number of iterations). If seed = "random", a random seed will be used, and P-values will vary. One can also specify an integer for specific seed values, which might be of interest for advanced users.
A logical value to indicate whether a progress bar should be printed to the screen. This is helpful for long-running analyses.
Objects of class "pls" from integration.test return a list of the following:
The estimate of morphological integration: PLS.corr. The mean of pairwise PLS correlations between partitions is used when there are more than two partitions.
The pairwise r.pls, if the number of partitions is greater than 2.
The empirically calculated P-value from the resampling procedure.
The singular vectors of the left (x) block (for 2 modules only).
The singular vectors of the right (y) block (for 2 modules only).
The correlation coefficients found in each random permutation of the resampling procedure.
Values of left (x) block projected onto singular vectors (for 2 modules only).
Values of right (y) block projected onto singular vectors (for 2 modules only).
The singular value decomposition of the cross-covariances (for 2 modules only).
Input values for the left block (for 2 modules only).
Input values for the right block (for 2 modules only).
Left block (matrix) found from A1 (for 2 modules only).
Right block (matrix) found from A2 (for 2 modules only).
The number of random permutations used in the resampling procedure.
The match call.
The function quantifies the degree of phylogenetic morphological integration between two or more sets of shape data as
defined by landmark coordinates. The approach is based on a Brownian motion model of evolution. It is
assumed that the landmarks have previously been aligned using
Generalized Procrustes Analysis (GPA) [e.g., with gpagen
].
The function estimates the degree of morphological covariation between two or sets of variables while accounting for phylogeny using partial least squares (Adams and Felice 2014), and under a Brownian motion model of evolution. If more than two partitions are defined, the average pairwise PLS correlation is utilized as the test statistic. The observed value is statistically assessed using permutation, where data for one partition are permuted relative to the other partitions. Note that this permutation is performed on phylogenetically- transformed data, so that the probability of phylogenetic association of A vs. B is similar to that of B vs. A: i.e., prob(A,B|phy)~prob(B,A|phy).
Input for the analysis can take one of two forms. First, one can input a single dataset (as a matrix or 3D array, along with a vector describing which variables correspond to which partitions (for the case of a 3D array, which landmarks belong to which partitions is specified). Alternatively, when evaluating the integration between two structures or partitions, two datasets may be provided.
The generic functions, print
, summary
, and plot
all work with phylo.integration
.
The generic function, plot
, produces a two-block.pls plot. This function calls plot.pls
, which has two additional
arguments (with defaults): label = NULL, warpgrids = TRUE. These arguments allow one to include a vector to label points and a logical statement to
include warpgrids, respectively. Warpgrids can only be included for 3D arrays of Procrustes residuals. The plot is a plot of PLS scores from
Block1 versus Block2 performed for the first set of PLS axes.
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.
data(plethspecies)
Y.gpa<-gpagen(plethspecies$land) #GPA-alignment
land.gps<-c("A","A","A","A","A","B","B","B","B","B","B")
IT<- phylo.integration(Y.gpa$coords,partition.gp=land.gps,phy=plethspecies$phy,iter=999)
summary(IT) # Test summary
plot(IT) # PLS plot
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