ortho_diss: A function for computing dissimilarity matrices from...

In resemble: Memory-Based Learning in Spectral Chemometrics

A function for computing dissimilarity matrices from orthogonal projections (ortho_diss)

Description

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This function computes dissimilarities (in an orthogonal space) between either observations in a given set or between observations in two different sets.The dissimilarities are computed based on either principal component projection or partial least squares projection of the data. After projecting the data, the Mahalanobis distance is applied.

Usage

ortho_diss(Xr, Xu = NULL,
           Yr = NULL,
           pc_selection = list(method = "var", value = 0.01),
           diss_method = "pca",
           .local = FALSE,
           pre_k,
           center = TRUE,
           scale = FALSE,
           compute_all = FALSE,
           return_projection = FALSE,
           allow_parallel = TRUE, ...)

Arguments

Xr	a matrix containing n reference observations rows and p variablescolumns.
Xu	an optional matrix containing data of a second set of observations with p variables/columns.
Yr	a matrix of n rows and one or more columns (variables) with side information corresponding to the observations in Xr (e.g. response variables). It can be numeric with multiple variables/columns, or character with one single column. This argument is required if: diss_method == 'pls': Yr is required to project the variables to orthogonal directions such that the covariance between the extracted pls components and Yr is maximized. pc_selection$method == 'opc': Yr is required to optimize the number of components. The optimal number of projected components is the one for which its distance matrix minimizes the differences between the Yr value of each observation and the Yr value of its closest observation. See sim_eval.
pc_selection	a list of length 2 which specifies the method to be used for optimizing the number of components (principal components or pls factors) to be retained. This list must contain two elements (in the following order): method (a character indicating the method for selecting the number of components) and value (a numerical value that complements the selected method). The methods available are: "opc": optimized principal component selection based on Ramirez-Lopez et al. (2013a, 2013b). The optimal number of components (of a given set of observations) is the one for which its distance matrix minimizes the differences between the Yr value of each observation and the Yr value of its closest observation. In this case, value must be a value (larger than 0 and below min(nrow(Xr) + nrow(Xu), ncol(Xr)) indicating the maximum number of principal components to be tested. See the ortho_projection function for more details. "cumvar": selection of the principal components based on a given cumulative amount of explained variance. In this case, value must be a value (larger than 0 and below or equal to 1) indicating the minimum amount of cumulative variance that the combination of retained components should explain. "var": selection of the principal components based on a given amount of explained variance. In this case, value must be a value (larger than 0 and below or equal to 1) indicating the minimum amount of variance that a single component should explain in order to be retained. "manual": for manually specifying a fix number of principal components. In this case, value must be a value (larger than 0 and below the minimum dimension of Xr or Xr and Xu combined). indicating the minimum amount of variance that a component should explain in order to be retained. Default is list(method = "var", value = 0.01). Optionally, the pc_selection argument admits "opc" or "cumvar" or "var" or "manual" as a single character string. In such case, the default "value" when either "opc" or "manual" are used is 40. When "cumvar" is used the default "value" is set to 0.99 and when "var" is used, the default "value" is set to 0.01.
diss_method	a character value indicating the type of projection on which the dissimilarities must be computed. This argument is equivalent to method argument in the ortho_projection function. Options are: "pca": principal component analysis using the singular value decomposition algorithm) "pca.nipals": principal component analysis using the non-linear iterative partial least squares algorithm. "pls": partial least squares. "mpls": modified partial least squares (Shenk and Westerhaus, 1991 and Westerhaus, 2014). See the ortho_projection function for further details on the projection methods.
.local	a logical indicating whether or not to compute the dissimilarities locally (i.e. projecting locally the data) by using the pre_k nearest neighbor observations of each target observation. Default is FALSE. See details.
pre_k	if .local = TRUE a numeric integer value which indicates the number of nearest neighbors to (pre-)retain for each observation to compute the (local) orthogonal dissimilarities to each observation in its neighborhhod.
center	a logical indicating if the Xr and Xu must be centered. If Xu is provided the data is centered around the mean of the pooled Xr and Xu matrices (\mjeqnXr \cup XuXr U Xu). For dissimilarity computations based on pls, the data is always centered for the projections.
scale	a logical indicating if the Xr and Xu must be scaled. If Xu is provided the data is scaled based on the standard deviation of the the pooled Xr and Xu matrices (\mjeqnXr \cup XuXr U Xu). if center = TRUE, scaling is applied after centering.
compute_all	a logical. In case Xu is specified it indicates whether or not the distances between all the elements resulting from the pooled Xr and Xu matrices (\mjeqnXr \cup XuXr U Xu must be computed).
return_projection	a logical. If TRUE the ortho_projection object on which the dissimilarities are computed will be returned. Default is FALSE. Note that for .local = TRUE only the initial projection is returned (i.e. local projections are not).
allow_parallel	a logical (default TRUE). It allows parallel computing of the local distance matrices (i.e. when .local = TRUE). This is done via foreach function of the 'foreach' package.
...	additional arguments to be passed to the ortho_projection function.

Details

When .local = TRUE, first a global dissimilarity matrix is computed based on the parameters specified. Then, by using this matrix for each target observation, a given set of nearest neighbors (pre_k) are identified. These neighbors (together with the target observation) are projected (from the original data space) onto a (local) orthogonal space (using the same parameters specified in the function). In this projected space the Mahalanobis distance between the target observation and its neighbors is recomputed. A missing value is assigned to the observations that do not belong to this set of neighbors (non-neighbor observations). In this case the dissimilarity matrix cannot be considered as a distance metric since it does not necessarily satisfies the symmetry condition for distance matrices (i.e. given two observations \mjeqnx_ix_i and \mjeqnx_jx_j, the local dissimilarity (\mjeqndd) between them is relative since generally \mjeqnd(x_i, x_j) \neq d(x_j, x_i)d(x_i, x_j) ne d(x_j, x_i)). On the other hand, when .local = FALSE, the dissimilarity matrix obtained can be considered as a distance matrix.

In the cases where "Yr" is required to compute the dissimilarities and if .local = TRUE, care must be taken as some neighborhoods might not have enough observations with non-missing "Yr" values, which might retrieve unreliable dissimilarity computations.

If "opc" or "manual" are used in pc_selection$method and .local = TRUE, the minimum number of observations with non-missing "Yr" values at each neighborhood is determined by pc_selection$value (i.e. the maximum number of components to compute).

Value

a list of class ortho_diss with the following elements:

• n_components: the number of components (either principal components or partial least squares components) used for computing the global dissimilarities.

• global_variance_info: the information about the expalined variance(s) of the projection. When .local = TRUE, the information corresponds to the global projection done prior computing the local projections.

• local_n_components: if .local = TRUE, a data.table which specifies the number of local components (either principal components or partial least squares components) used for computing the dissimilarity between each target observation and its neighbor observations.

• dissimilarity: the computed dissimilarity matrix. If .local = FALSE a distance matrix. If .local = TRUE a matrix of class local_ortho_diss. In this case, each column represent the dissimilarity between a target observation and its neighbor observations.

• projection: if return_projection = TRUE, an ortho_projection object.

Author(s)

Leonardo Ramirez-Lopez

References

Ramirez-Lopez, L., Behrens, T., Schmidt, K., Stevens, A., Dematte, J.A.M., Scholten, T. 2013a. The spectrum-based learner: A new local approach for modeling soil vis-NIR spectra of complex data sets. Geoderma 195-196, 268-279.

Ramirez-Lopez, L., Behrens, T., Schmidt, K., Viscarra Rossel, R., Dematte, J. A. M., Scholten, T. 2013b. Distance and similarity-search metrics for use with soil vis-NIR spectra. Geoderma 199, 43-53.

See Also

ortho_projection, sim_eval

Examples

library(prospectr)
data(NIRsoil)

Xu <- NIRsoil$spc[!as.logical(NIRsoil$train), ]
Yu <- NIRsoil[!as.logical(NIRsoil$train), "CEC", drop = FALSE]
Yr <- NIRsoil[as.logical(NIRsoil$train), "CEC", drop = FALSE]
Xr <- NIRsoil$spc[as.logical(NIRsoil$train), ]

Xu <- Xu[!is.na(Yu), ]
Yu <- Yu[!is.na(Yu), , drop = FALSE]

Xr <- Xr[!is.na(Yr), ]
Yr <- Yr[!is.na(Yr), , drop = FALSE]

# Computation of the orthogonal dissimilarity matrix using the
# default parameters
pca_diss <- ortho_diss(Xr, Xu)

# Computation of a principal component dissimilarity matrix using
# the "opc" method for the selection of the principal components
pca_diss_optim <- ortho_diss(
  Xr, Xu, Yr,
  pc_selection = list("opc", 40),
  compute_all = TRUE
)

# Computation of a partial least squares (PLS) dissimilarity
# matrix using the "opc" method for the selection of the PLS
# components
pls_diss_optim <- ortho_diss(
  Xr = Xr, Xu = Xu,
  Yr = Yr,
  pc_selection = list("opc", 40),
  diss_method = "pls"
)

resemble documentation built on May 29, 2024, 8:49 a.m.