mds_test: Test optimal number of MDS dimensions.

In nzilbb.vowels: Vowel Covariation Tools

Test optimal number of MDS dimensions.

Description

Generate bootstrapped confidence intervals and permutation based null distribution for MDS analysis. Output shows how much stress is reduced by adding an additional dimension to the MDS analysis of dissimilarity_matrix, and bootstrapped iterations of dissimilarity_matrix, compared with the stress reduction expected from a matrix with no meaningful structure. This function is inspired by pca_test(), but is less connected with statistical literature than that function. We currently reject additional dimensions is they reduce less stress than we would expect by chance. That is, when the distribution from the boostrapped analyses sits notably lower than the permuted distribution when plotted by plot_mds_test()

Usage

mds_test(
  dissimilarity_matrix,
  n_boots = 50,
  n_perms = 50,
  test_dimensions = 5,
  principal = TRUE,
  mds_type = "ordinal",
  spline_degree = 2,
  spline_int_knots = 2,
  ...
)

Arguments

dissimilarity_matrix	Square matrix of dissimilarity scores.
n_boots	Number of bootstrapping iterations (default: 25).
n_perms	Number of permutations (default: 25).
test_dimensions	Number of MDS dimensions to test for stress reduction (default: 5).
principal	Whether to apply principal axis transform to MDS (default: TRUE)
mds_type	What kind of MDS to apply, see smacof::smacofSym() (default: 'ordinal')
spline_degree	How many spline degrees when type is 'mspline' (default: 2)
spline_int_knots	How many internal knots when type is 'mspline' (default: 2)
...	Arguments passed to smacof::smacofSym()

Value

object of class mds_test_results, containing:

• ⁠$stress_reduction⁠ a tibble containing

• ⁠$n_boots⁠ Number of bootstrapping iterations.

• ⁠$n_perms⁠ Number of permutation iterations

• ⁠$mds_type⁠ Type of MDS analysis (type argument passed to smacof::smacofSym())

• ⁠$principal⁠ Whether principal axis transformation is applied (passed to smacof::smacofSym())

Examples

# Apply interval MDS to `sim_matrix`, with 5 permutations and bootstraps
# testing up to 3 dimensions. In real usage, increase `n_boots` and `n_perms`
# to at least 50.
mds_test(
 smacof::sim2diss(sim_matrix, method="reverse"),
 n_boots = 5,
 n_perms = 5,
 test_dimensions = 3,
 mds_type = 'interval'
)

nzilbb.vowels documentation built on June 8, 2025, 12:35 p.m.