distMatSP: Calculate a multidimensional distance matrix between two...

In sarp.snowprofile.alignment: Snow Profile Alignment, Aggregation, and Clustering

Calculate a multidimensional distance matrix between two profiles

Description

This routine calculates a distance matrix for two given profiles (query and ref). Analogously to other DTW routines, the query is arranged along the matrix rows, the ref along the columns. Every cell of the matrix represents the distance between the corresponding profile layers. The distance is calculated based on the specified layer properties (e.g., hardness, gtype, ddate). The routine calls subroutines to calculate the distance for each property and combines the normalized distances by weighted averaging.

Usage

distMatSP(
  query,
  ref,
  dims = c("hardness", "gtype"),
  weights = c(0.2, 0.8),
  gtype_distMat = sim2dist(grainSimilarity_align(FALSE)),
  prefLayerWeights = layerWeightingMat(FALSE),
  ddateNorm = 5,
  windowFunction = warpWindowSP,
  top.down.mirroring = FALSE,
  warn.if.na.in.distance.calc = FALSE,
  ...
)

Arguments

query	The query snowprofile object
ref	The ref snowprofile object
dims	Character vector containing the layer properties to calculate the distance over. Currently implemented are the properties hardness, gtype, ddate, density, ogs.
weights	Numeric vector of the same length as dims specifying the averaging weights to each element of dims.
gtype_distMat	A symmetric distance scoring matrix provided as data.frame that stores information about the distances between the encountered grain types of the provided profiles. Default is the corresponding distance matrix of grainSimilarity_align, cf. sim2dist.
prefLayerWeights	A matrix similar to gtype_distMat, but storing weights for preferential layer matching, e.g. defaults to layerWeightingMat; the higher the values for a given grain type pair, the more the algorithm will try to match those layers above others. To turn weighting scheme off, set prefLayerWeights = NA
ddateNorm	Normalize the deposition date distance by ddateNorm number of days. Numeric, default 5.
windowFunction	a window function analogous to warpWindowSP (Other compatible window functions can be found in dtw::dtwWindowingFunctions.)
top.down.mirroring	Will the resulting distance matrix be used for top down alignments? i.e., do you want to mirror the matrix about its anti-diagonal (top-left/bottom-right diagonal)?
warn.if.na.in.distance.calc	most dependent functions in this package should be able to deal with NA values encountered in distance calculations. Set this argument to TRUE if you want to be warned anyways.
...	arguments to the window function, e.g. window.size, window.size.abs, ddate.window.size, ...

Value

A distance matrix of dimension (n x m), where n, m are the number of layers in the query and ref, respectively.

Note

For package developers: dot inputs to the function (i.e., ...) also necessary to keep dtwSP highly flexible and customizable. Dot inputs may contain arguments that remain unused in this function.

Author(s)

fherla

See Also

resampleSPpairs

Examples

## call function with two snow profiles of unequal lengths, without using a window function:
dMat_noWindow <- distMatSP(SPpairs$A_modeled, SPpairs$A_manual, windowFunction = NA)
graphics::image(dMat_noWindow, main = "Default distance matrix without a warping window")


## compute distance based on grain type alone,
## and additionally disable preferential layer matching:
dMat <- distMatSP(SPpairs$A_modeled, SPpairs$A_manual, windowFunction = NA,
                  dims = "gtype", weights = 1, prefLayerWeights = NA)
graphics::image(dMat,
                main = "Only based on grain type, and without preferential layer matching")

## enable preferential layer matching:
dMat <- distMatSP(SPpairs$A_modeled, SPpairs$A_manual, windowFunction = NA)
graphics::image(dMat,
                main = "... with preferential layer matching")


## using a warping window:
dMat <- distMatSP(SPpairs$A_modeled, SPpairs$A_manual, window.size.abs = 50)
graphics::image(dMat, main = "... and superimposing an absolute warping window of 50 cm")

sarp.snowprofile.alignment documentation built on Aug. 8, 2022, 1:05 a.m.