尺度法とその関連領域:多次元尺度法の研究に関する最近の動向 (2)

Multidimensional scaling (MDS) represents a family of various spatial geometric models for the multidimensional representation of the structure in data as well as the corresponding set of methods for fitting such spatial models. Its major uses in Marketing include positioning, market segmentation, new product design, consumer preference analysis, etc. We present several popular MOS models for the analysis of consumer preference or dominance data. The first spatial model presented is called the vector or scalar products model which represents brands by points and consumers by vectors in a T dimensional derived joint space. We describe both individual and segment level vector MDS models. The second spatial model is called the multidimensional simple unfolding or ideal point model where both brands and consumers are jointly represented by points in a T dimensional derived joint space. We briefly discuss two more complex variants of multidimensional unfolding called the weighted unfolding model and the general unfolding model. Here too, we describe both individual and segment level unfolding MOS models. We contrast the underlying utility assumptions implied by each of these models with illustrative figures of typical joint spaces derived from each approach. An actual commercial application of consideration to buy large Sports Utility Vehicle (SUV) vehicles is provided with the empirical results from each major type of model at the individual level is discussed.

Introduction.- Data management and software.- Advice for teachers.- Exploration.- Linear regression.- Generalised linear modelling.- Additive and generalised additive modelling.- Introduction to mixed modelling.- Univariate tree models.- Measures of association.- Ordination--first encounter.- Principal component analysis and redundancy analysis.- Correspondence analysis and canonical correspondence analysis.- Introduction to discriminant analysis.- Principal coordinate analysis and non-metric multidimensional scaling.- Time series analysis--Introduction.- Common trends and sudden changes.- Analysis and modelling lattice data.- Spatially continuous data analysis and modelling.- Univariate methods to analyse abundance of decapod larvae.- Analysing presence and absence data for flatfish distribution in the Tagus estuary, Portugual.- Crop pollination by honeybees in an Argentinean pampas system using additive mixed modelling.- Investigating the effects of rice farming on aquatic birds with mixed modelling.- Classification trees and radar detection of birds for North Sea wind farms.- Fish stock identification through neural network analysis of parasite fauna.- Monitoring for change: using generalised least squares, nonmetric multidimensional scaling, and the Mantel test on western Montana grasslands.- Univariate and multivariate analysis applied on a Dutch sandy beach community.- Multivariate analyses of South-American zoobenthic species--spoilt for choice.- Principal component analysis applied to harbour porpoise fatty acid data.- Multivariate analysis of morphometric turtle data--size and shape.- Redundancy analysis and additive modelling applied on savanna tree data.- Canonical correspondence analysis of lowland pasture vegetation in the humid tropics of Mexico.- Estimating common trends in Portuguese fisheries landings.- Common trends in demersal communities on the Newfoundland-Labrador Shelf.- Sea level change and salt marshes in the Wadden Sea: a time series analysis.- Time series analysis of Hawaiian waterbirds.- Spatial modelling of forest community features in the Volzhsko-Kamsky reserve.

Detecting significant change in stream benthic macroinvertebrate communities in wilderness areas

A natural extension of classical metric multidimensional scaling is proposed. The result is a new formulation of nonmetric multidimensional scaling in which the strain criterion is minimized subject to order constraints on the disparity variables. Innovative features of the new formulation include: the parametrization of the p-dimensional distance matrices by the positive semidefinite matrices of rank ≤p; optimization of the (squared) disparity variables, rather than the configuration coordinate variables; and a new nondegeneracy constraint, which restricts the set of (squared) disparities rather than the set of distances. Solutions are obtained using an easily implemented gradient projection method for numerical optimization. The method is applied to two published data sets.

Dimension reduction has been used to visualise the distribution of multidimensional microbiome data, but the composite variables calculated by the dimension reduction methods have not been widely used to investigate the relationship of the human gut microbiome with lifestyle and disease. In the present study, we applied several dimension reduction methods, including principal component analysis, principal coordinate analysis (PCoA), non-metric multidimensional scaling (NMDS), and non-negative matrix factorization, to a microbiome dataset from 186 subjects with symptoms of allergic rhinitis (AR) and 106 controls. All the dimension reduction methods supported that the distribution of microbial data points appeared to be continuous rather than discrete. Comparison of the composite variables calculated from the different dimension reduction methods showed that the characteristics of the composite variables differed depending on the distance matrices and the dimension reduction methods. The first composite variables calculated from PCoA and NMDS with the UniFrac distance were strongly associated with AR (FDR adjusted P = 2.4 × 10–4 for PCoA and P = 2.8 × 10–4 for NMDS), and also with the relative abundance of Bifidobacterium and Prevotella. The abundance of Bifidobacterium was also linked to intake of several nutrients, including carbohydrate, saturated fat, and alcohol via composite variables. Notably, the association between the composite variables and AR was much stronger than the association between the relative abundance of individual genera and AR. Our results highlight the usefulness of the dimension reduction methods for investigating the association of microbial composition with lifestyle and disease in clinical research.

Four relatively homogeneous field data sets were analyzed, representing boreal, heath-like forest-floor and rock vegetation in Finland, corresponding to Finnish Calluna and Cladina site types. The methods used were principal component analysis (PCA) of covariance matrices, orthogonal correspondence analysis or reciprocal averaging (RA), detrended correspondence analysis (DCA), and linear and nonmetric multidimensional scaling (MDS). RA and DCA gave ordinations in which every species had nearly equal weight. MDS and PCA gave results determined mostly by a few dominant species. MDS and PCA ordinations were very similar to RA and DCA ones when the original data were standardized so that for each species the mean of positive occurrences was the same while quantitative differences within species were retained. RA and PCA were generally very good and reliable, providing that the impact of rare species and outlier releves was removed in RA. DCA was slightly less reliable than RA. MDS was sensitive to uneven sampling patterns and was the least reliable method compared.

Preface. Acknowledgments. 1 Introduction. 1.1 The nature of paleontological data. 1.2 Advantages and pitfalls of paleontological data analysis. 1.3 Software. 2 Basic statistical methods. 2.1 Introduction. 2.2 Statistical distributions. 2.3 Shapiro-Wilk test for normal distribution. 2.4 F test for equality of variances. 2.5 Student's t test and Welch test for equality of means. 2.6 Mann-Whitney U test for equality of medians. 2.7 Kolmogorov-Smirnov test for equality of distributions. 2.8 Permutation and resampling. 2.9 One-way ANOVA. 2.10 Kruskal-Wallis test. 2.11 Linear correlation. 2.12 Non-parametric tests for correlation. 2.13 Linear regression. 2.14 Reduced major axis regression. 2.15 Nonlinear curve fitting. 2.16 Chi-square test. 3 Introduction to multivariate data analysis. 3.1 Approaches to multivariate data analysis. 3.2 Multivariate distributions. 3.3 Parametric multivariate tests. 3.4 Non-parametric multivariate tests. 3.5 Hierarchical cluster analysis. 3.5 K-means cluster analysis. 4 Morphometrics. 4.1 Introduction. 4.2 The allometric equation. 4.3 Principal components analysis (PCA). 4.4 Multivariate allometry. 4.5 Discriminant analysis for two groups. 4.6 Canonical variate analysis (CVA). 4.7 MANOVA. 4.8 Fourier shape analysis. 4.9 Elliptic Fourier analysis. 4.10 Eigenshape analysis. 4.11 Landmarks and size measures. 4.12 Procrustean fitting. 4.13 PCA of landmark data. 4.14 Thin-plate spline deformations. 4.15 Principal and partial warps. 4.16 Relative warps. 4.17 Regression of partial warp scores. 4.18 Disparity measures. 4.19 Point distribution statistics. 4.20 Directional statistics. Case study: The ontogeny of a Silurian trilobite. 5 Phylogenetic analysis. 5.1 Introduction. 5.2 Characters. 5.3 Parsimony analysis. 5.4 Character state reconstruction. 5.5 Evaluation of characters and tree topologies. 5.6 Consensus trees. 5.7 Consistency index. 5.8 Retention index. 5.9 Bootstrapping. 5.10 Bremer support. 5.11 Stratigraphical congruency indices. 5.12 Phylogenetic analysis with Maximum Likelihood. Case study: The systematics of heterosporous ferns. 6 Paleobiogeography and paleoecology. 6.1 Introduction. 6.2 Diversity indices. 6.3 Taxonomic distinctness. 6.4 Comparison of diversity indices. 6.5 Abundance models. 6.6 Rarefaction. 6.7 Diversity curves. 6.8 Size-frequency and survivorship curves. 6.9 Association similarity indices for presence/absence data. 6.10 Association similarity indices for abundance data. 6.11 ANOSIM and NPMANOVA. 6.12 Correspondence analysis. 6.13 Principal Coordinates analysis (PCO). 6.14 Non-metric Multidimensional Scaling (NMDS). 6.15 Seriation. Case study: Ashgill brachiopod paleocommunities from East China. 7 Time series analysis. 7.1 Introduction. 7.2 Spectral analysis. 7.3 Autocorrelation. 7.4 Cross-correlation. 7.5 Wavelet analysis. 7.6 Smoothing and filtering. 7.7 Runs test. Case study: Sepkoski's generic diversity curve for the Phanerozoic. 8 Quantitative biostratigraphy. 8.1 Introduction. 8.2 Parametric confidence intervals on stratigraphic ranges. 8.3 Non-parametric confidence intervals on stratigraphic ranges. 8.4 Graphic correlation. 8.5 Constrained optimisation. 8.6 Ranking and scaling. 8.7 Unitary Associations. 8.8 Biostratigraphy by ordination. 8.9 What is the best method for quantitative biostratigraphy?. Appendix A: Plotting techniques. Appendix B: Mathematical concepts and notation. References. Index

The usual convergence proof of the SMACOF algorithm model for least squares multidimensional scaling critically depends on the assumption of nonnegativity of the quantities to be fitted, called the pseudodistances. When this assumption is violated, erratic convergence behavior is known to occur. Three types of circumstances in which some of the pseudodistances may become negative are outlined: nonmetric multidimensional scaling with normalization on the variance, metric multidimensional scaling including an additive constant, and multidimensional scaling under the city-block distance model. A generalization of the SMACOF method is proposed to resolve the difficulty that is based on the same rationale frequently involved in robust fitting with least absolute residuals.

Estimation of the covariance structure of spatial processes is a fundamental prerequisite for problems of spatial interpolation and the design of monitoring networks. We introduce a nonparametric approach to global estimation of the spatial covariance structure of a random function Z(x, t) observed repeatedly at times ti (i = 1, …, T) at a finite number of sampling stations xi (i = 1, 2, …, N) in the plane. Our analyses assume temporal stationarity but do not assume spatial stationarity (or isotropy). We analyze the spatial dispersions var(Z(xi, t) − Z(xj, t)) as a natural metric for the spatial covariance structure and model these as a general smooth function of the geographic coordinates of station pairs (xi, xj ). The model is constructed in two steps. First, using nonmetric multidimensional scaling (MDS) we compute a two-dimensional representation of the sampling stations for which a monotone function of interpoint distances δij approximates the spatial dispersions. MDS transforms the problem into one for which the covariance structure, expressed in terms of spatial dispersions, is stationary and isotropic. Second, we compute thin-plate splines to provide smooth mappings of the geographic representation of the sampling stations into their MDS representation. The composition of this mapping f and a monotone function g derived from MDS yields a nonparametric estimator of var(Z(xa, t) − Z(xb, t)) for any two geographic locations xa and xb (monitored or not) of the form g(|f(xa ) − f(xb )|). By restricting the monotone function g to a class of conditionally nonpositive definite variogram functions, we ensure that the resulting nonparametric model corresponds to a nonnegative definite covariance model. We use biorthogonal grids, introduced by Bookstein in the field of morphometrics, to depict the thin-plate spline mappings that embody the nature of the anisotropy and nonstationarity in the sample covariance matrix. An analysis of mesoscale variability in solar radiation monitored in southwestern British Columbia demonstrates this methodology.

The well-known individual differences scaling (INDSCAL) model is intended for simultaneous metric multidimensional scaling (MDS) of several doubly centered matrices of squared dissimilarities. In this work, the problem of fitting the orthogonal INDSCAL model to the data is reformulated and studied as a matrix optimization problem on the product manifold of orthonormal and diagonal matrices. A Riemannian inexact Newton method is proposed to address the underlying problem, with the global and quadratic convergence of the proposed method established under some mild assumptions. Furthermore, the positive definiteness condition of the Riemannian Hessian of the objective function at a solution is derived. Some numerical experiments are provided to illustrate the efficiency of the proposed method. Mathematics subject classification: 15A24; 15A57; 65F10; 65F30

Pimentel, R. A. (Department of Biological Sciences, California Polytechnic State Univ., San Luis Obispo, California) 1981. A comparative study of data and ordination techniques based on a hybrid swarm of sand verbenas (Abronia Juss.). Syst. Zool., 30:250-267.-The influence of kinds of variables, data errors, standardizations similarity coefficients, and ordination techniques are judged in reference to a model involving hybridization and introgression in three species of sand verbenas, Abronia (Juss.). Various criteria indicate that principal component analysis performs best, but inaccurately, with variable standardization and the correlation matrix, and that nonlinear mapping consistently performs poorly. Excellent results were obtained from principal coordinate analysis with Gower's general similarity coefficient based upon quantitative and multistate variables; a 'diagnostic' character measured with known error; and detailed color evaluation. This and other principal coordinate analysis results were further improved by nonmetric multidimensional scaling. Performance of methods is consistent with the nonlinearity of Abronia data. It is assumed that nonlinearity is common in taxonomic data. [Multivariate analysis; multivariate analysis assumptions; discriminant analysis; classification methods; principal component analysis; principal coQrdinate analysis; nonlinear mapping; nonmetric multidimensional scaling; ordination comparisons; data properties; nonlinearity; sand verbenas, Abronia.]

Acacia decurrens, originally from Australia, is a woody plant that has become a concern in the erupted areas of Merapi volcano in 2006. The purpose of this study was to quantitatively describe the ecology of Acacia decurrens, and its invasive potential. Vegetation analysis was carried out in four areas of Mount Merapi National Park (TNGM), namely Kalikuning, Kaliadem, Plawangan and Pranajiwa. Ordination using the Non Metric Multidimensional Scaling (NMDS) method and Canonical Correspondence (CCA) and Spearman's bivariate correlation were carried out in data analysis. The results of NMDS analysis (2D stress = 0.14) showed that open areas due to eruption in Kaliadem are now dominated by A. decurrens. The results of the analysis also showed a significant negative correlation (Spearman rho = 0.6) between the abundance of A. decurrens and the level of species diversity in the sampling location. From the results of CCA, A. decurrens in the seedling stage appeared to coexist with other types of ground cover such as Alangium javanicum and Araliaceae. But in the tree phase, this species tended to form pure stands and only occasionally appeared to live side by side with other types of Fabaceae such as Albizia lopantha. Tree-level A. decurrens seemed to prefer sites with lower pH levels while A. decurrens seedling levels were more commonly found in sites with higher pH. Acacia decurrens have the potential to become a weed in TNGM due to its dominant distribution and tendency to decrease the level of species diversity in TNGM.

11 Applications of Multidimensional Scaling in Psychometrics

Multidimensional scaling (MDS) is a popular tool for dimensionality reduction and data visualization. Given distances between data points and a target low-dimension, the MDS problem seeks to find a configuration of these points in the low-dimensional space, such that the inter-point distances are preserved as well as possible. We focus on the most common approach to formulate the MDS problem, known as stress minimization, which results in a challenging non-smooth and non-convex optimization problem. In this paper, we propose an inertial version of the well-known SMACOF Algorithm, which we call AI-SMACOF. This algorithm is proven to be globally convergent, and to the best of our knowledge this is the first result of this kind for algorithms aiming at solving the stress MDS minimization. In addition to the theoretical findings, numerical experiments provide another evidence for the superiority of the proposed algorithm.

Two instruments were used to evaluate an agency's type and availability of services for HIV-positive and at-risk adolescents, and to assess opinions concerning healthcare referral patterns. These instruments were administered to representatives of 22 agencies from 10 categories of healthcare services. Nonmetric multidimensional scaling was used to model ratings of interagency knowledge, referral patterns, and general satisfaction with services. We found that no agencies offered youth services for inpatient adolescent-specific mental health treatment or short-term residential drug treatment; however, few offered long-term residential substance abuse detoxification services (5%), outpatient drug maintenance (5%), HIV-specific inpatient services (9%), intensive day treatment for substance abusers (9%), HIV home care (14%), HIV hospice care (14%), inpatient medical services (14%), short-term shelters (14%), long-term housing (18%), HIV-specific clinical trials (18%), and dental services (23%). Barriers to expanding care included lack of funding, transportation, and lack of awareness among youths about services. A multidimensional scaling analysis identified a tight service cluster of two community health centers and the largest public hospital serving poor communities of color, as well as a relatively tight cluster of three service agencies located on the Boston Common serving homeless youths. A third service cluster consisted of two university-affiliated medical centers and one community health center. In conclusion, we found that many critical services for HIV-positive youths are relatively scarce. Multidimensional scaling provides a visual presentation of the relationships of network sites. This evaluation of services indicates a need for increased, accessible youth-oriented HIV services and suggests that linkages across the three distinct clusters of service providers should be solidified. These methodologies can be used to develop a generic model describing the stages of linkage formation in HIV care service networks.