Just a wrapper for svd() that returns an adequate output
when used on blocks of variables. Can deal with phylogenetic data too
using ape and phytools functions. Used internally.
svd_block(x, y, tree = NULL)First block of variables
Second block of variables
An optional "phylo" object containing a phylogenetic
tree whose tip.labels match rownames of x and y.
Mimics the svd() output.
#laod data and packages
library(geomorph)
data("tails")
shapes <- tails$shapes
sizes <- tails$sizes
species <- tails$data$species
tree <- tails$tree
sp_shapes <- expected_shapes(shapes, species)[,,tree$tip.label]
sp_sizes <- cbind(tapply(sizes, species, mean))[tree$tip.label,]
#perform partial svd
svd_block(x = sizes, y = two.d.array(shapes))
#> $d
#> [1] 42.92575
#>
#> $v
#> [,1]
#> [1,] -5.613140e-02
#> [2,] 1.220262e-01
#> [3,] -5.613140e-02
#> [4,] -1.220262e-01
#> [5,] 2.042085e-02
#> [6,] 1.341861e-01
#> [7,] 2.042085e-02
#> [8,] -1.341861e-01
#> [9,] -4.132683e-01
#> [10,] -1.266548e-01
#> [11,] 8.369095e-02
#> [12,] 5.318992e-02
#> [13,] 7.305758e-01
#> [14,] -1.136551e-08
#> [15,] 8.369094e-02
#> [16,] -5.318994e-02
#> [17,] -4.132683e-01
#> [18,] 1.266548e-01
#>
#> $u
#> [,1]
#> [1,] 1
#>
#perform partial svd on phylogenetic structure
svd_block(x = sp_sizes, y = two.d.array(sp_shapes), tree = tree)
#> $d
#> [1] 17.05874
#>
#> $v
#> [,1]
#> [1,] -7.089075e-02
#> [2,] 1.199741e-01
#> [3,] -7.089075e-02
#> [4,] -1.199741e-01
#> [5,] 1.607633e-03
#> [6,] 1.287336e-01
#> [7,] 1.607636e-03
#> [8,] -1.287336e-01
#> [9,] -3.125015e-01
#> [10,] -1.063445e-01
#> [11,] -3.778528e-02
#> [12,] -3.916476e-02
#> [13,] 8.391398e-01
#> [14,] 1.094144e-08
#> [15,] -3.778528e-02
#> [16,] 3.916475e-02
#> [17,] -3.125015e-01
#> [18,] 1.063445e-01
#>
#> $u
#> [,1]
#> [1,] 1
#>