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QTS Distance Matrix Computation

Source: R/qts-dist.R
dist.Rd

This function massages an input sample of quaternion time series to turn it into a pairwise distance matrix.

Usage

dist(x, metric, ...)

# Default S3 method
dist(
  x,
  metric = c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski"),
  diag = FALSE,
  upper = FALSE,
  p = 2,
  ...
)

# S3 method for class 'qts_sample'
dist(
  x,
  metric = c("l2", "normalized_l2", "pearson", "dtw"),
  is_domain_interval = FALSE,
  transformation = c("identity", "srvf"),
  warping_class = c("none", "shift", "dilation", "affine", "bpd"),
  rotation_invariance = FALSE,
  cluster_on_phase = FALSE,
  labels = NULL,
  ncores = 1L,
  ...
)

Arguments

x

A numeric matrix, data frame, stats::dist object or object of class qts_sample specifying the sample on which to compute the pairwise distance matrix.

metric

A character string specifying the distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski" if x is not a QTS sample. Otherwise, it must be one of "l2", "pearson" or "dtw".

...

not used.

diag

logical value indicating whether the diagonal of the distance matrix should be printed by print.dist.

upper

logical value indicating whether the upper triangle of the distance matrix should be printed by print.dist.

p

The power of the Minkowski distance.

is_domain_interval

A boolean specifying whether the sample of curves is defined on a fixed interval. Defaults to FALSE.

transformation

A string specifying the transformation to apply to the original sample of curves. Choices are no transformation (transformation = "identity") or square-root velocity function transformation = "srvf". Defaults to "identity".

warping_class

A string specifying the class of warping functions. Choices are no warping (warping_class = "none"), shift y = x + b (warping_class = "shift"), dilation y = ax (warping_class = "dilation"), affine y = ax + b (warping_class = "affine") or boundary-preserving diffeomorphism (warping_class = "bpd"). Defaults to "none".

rotation_invariance

A boolean value specifying whether the distance should be invariant to rotation. This is only relevant when is_domain_interval is TRUE and transformation is "srvf" and warped_class is "bpd". Defaults to FALSE.

cluster_on_phase

A boolean specifying whether clustering should be based on phase variation or amplitude variation. Defaults to FALSE which implies amplitude variation.

labels

A character vector specifying curve labels. Defaults to NULL which uses sequential numbers as labels.

ncores

An integer value specifying the number of cores to use for parallel computation. Defaults to 1.

Value

An object of class stats::dist.

Examples

D <- dist(vespa64$igp[1:5])