distsd: Calculates the distance standard deviation...

View source: R/distcov_function.R

distsdR Documentation

Calculates the distance standard deviation \insertCiteedelmann2017distancedcortools.

Description

Calculates the distance standard deviation \insertCiteedelmann2017distancedcortools.

Usage

distsd(
  X,
  affine = FALSE,
  standardize = FALSE,
  bias.corr = FALSE,
  type.X = "sample",
  metr.X = "euclidean",
  use = "all",
  algorithm = "auto"
)

Arguments

X

contains either the sample or its corresponding distance matrix.

In the first case, X can be provided either as a vector (if one-dimensional), a matrix or a data.frame (if two-dimensional or higher).

In the second case, the input must be a distance matrix corresponding to the sample of interest.

If X is a sample, type.X must be specified as "sample". If X is a distance matrix, type.X must be specified as "distance".

affine

logical; specifies if the affinely invariant distance standard deviation \insertCitedueck2014affinelydcortools should be calculated or not.

standardize

logical; specifies if X and Y should be standardized dividing each component by its standard deviations. No effect when affine = TRUE.

bias.corr

logical; specifies if the bias corrected version of the sample distance standard deviation \insertCitehuo2016fastdcortools should be calculated.

type.X

For "distance", X is interpreted as a distance matrix. For "sample", X is interpreted as a sample.

metr.X

specifies the metric which should be used to compute the distance matrix for X (ignored when type.X = "distance").

Options are "euclidean", "discrete", "alpha", "minkowski", "gaussian", "gaussauto", "boundsq" or user-specified metrics (see examples).

For "alpha", "minkowski", "gaussian", "gaussauto" and "boundsq", the corresponding parameters are specified via "c(metric, parameter)", e.g. c("gaussian", 3) for a Gaussian metric with bandwidth parameter 3; the default parameter is 2 for "minkowski" and "1" for all other metrics.

See \insertCitelyons2013distance,sejdinovic2013equivalence,bottcher2017detecting;textualdcortools for details.

use

specifies how to treat missing values. "complete.obs" excludes observations containing NAs, "all" uses all observations.

algorithm

specifies the algorithm used for calculating the distance standard deviation.

"fast" uses an O(n log n) algorithm if the observations are one-dimensional and metr.X and metr.Y are either "euclidean" or "discrete", see also \insertCitehuo2016fast;textualdcortools.

"memsave" uses a memory saving version of the standard algorithm with computational complexity O(n^2) but requiring only O(n) memory.

"standard" uses the classical algorithm. User-specified metrics always use the classical algorithm.

"auto" chooses the best algorithm for the specific setting using a rule of thumb.

Value

numeric; the distance standard deviation of X.

References

\insertRef

bottcher2017detectingdcortools

\insertRef

dueck2014affinelydcortools

\insertRef

edelmann2017distancedcortools

\insertRef

huo2016fastdcortools

\insertRef

lyons2013distancedcortools

\insertRef

sejdinovic2013equivalencedcortools

\insertRef

szekely2007dcortools

\insertRef

szekely2009browniandcortools

Examples

X <- rnorm(100)
distsd(X) # for more examples on the options see the documentation of distcov.

dcortools documentation built on Dec. 8, 2022, 1:11 a.m.