Statistical Methods for the Qualitative Assessment of Dynamic Models with Time Delay (R Package qualV)

Results of ecological models differ, to some extent, more from measured data than from empirical knowledge. Existing techniques for validation based on quantitative assessments sometimes cause an underestimation of the performance of models due to time shifts, accelerations and delays or systematic differences between measurement and simulation. However, for the application of such models it is often more important to reproduce essential patterns instead of seemingly exact numerical values. This paper presents techniques to identify patterns and numerical methods to measure the consistency of patterns between observations and model results. An orthogonal set of deviance measures for absolute, relative and ordinal scale was compiled to provide informations about the type of difference. Furthermore, two different approaches accounting for time shifts were presented. The first one transforms the time to take time delays and speed differences into account. The second one describes known qualitative criteria dividing time series into interval units in accordance to their main features. The methods differ in their basic concepts and in the form of the resulting criteria. Both approaches and the deviance measures discussed are implemented in an R package. All methods are demonstrated by means of water quality measurements and simulation data. The proposed quality criteria allow to recognize systematic differences and time shifts between time series and to conclude about the quantitative and qualitative similarity of patterns.

Statistical Methods for the Qualitative Assessment of Dynamic Models with Time Delay (R Package qualV)

Results of ecological models differ, to some extent, more from measured data than from empirical knowledge. Existing techniques for validation based on quantitative assessments sometimes cause an underestimation of the performance of models due to time shifts, accelerations and delays or systematic differences between measurement and simulation. However, for the application of such models it is often more important to reproduce essential patterns instead of seemingly exact numerical values. This paper presents techniques to identify patterns and numerical methods to measure the consistency of patterns between observations and model results. An orthogonal set of deviance measures for absolute, relative and ordinal scale was compiled to provide informations about the type of difference. Furthermore, two different approaches accounting for time shifts were presented. The first one transforms the time to take time delays and speed differences into account. The second one describes known qualitative criteria dividing time series into interval units in accordance to their main features. The methods differ in their basic concepts and in the form of the resulting criteria. Both approaches and the deviance measures discussed are implemented in an R package. All methods are demonstrated by means of water quality measurements and simulation data. The proposed quality criteria allow to recognize systematic differences and time shifts between time series and to conclude about the quantitative and qualitative similarity of patterns

The compositional meaning of a detection limit

In compositional data analysis a value below detection limit (BDL) is typically modeled as the definitive information that the actual value is below some fixed value - the detection limit (see e.g. Palarea- Albaladejo et. al (2007, 2008)). Analytical chemistry (Heinrichs and Herrmann (1990); Fletcher (1981); Kellner et al. (2004)) however has a different view on measured concentrations. The measured concentration Cm is not the true concentration cm of the measurant but a quantity computed from an observable quantity Om through a calibration equation

Aitchison Geometry for Probability and Likelihood as a new approach to mathematical statistics

The Aitchison vector space structure for the simplex is generalized to a Hilbert space structure A2(P) for distributions and likelihoods on arbitrary spaces. Centralnotations of statistics, such as Information or Likelihood, can be identified in the algebraical structure of A2(P) and their corresponding notions in compositional data analysis, such as Aitchison distance or centered log ratio transform.In this way very elaborated aspects of mathematical statistics can be understoodeasily in the light of a simple vector space structure and of compositional data analysis. E.g. combination of statistical information such as Bayesian updating,combination of likelihood and robust M-estimation functions are simple additions/perturbations in A2(Pprior). Weighting observations corresponds to a weightedaddition of the corresponding evidence.Likelihood based statistics for general exponential families turns out to have aparticularly easy interpretation in terms of A2(P). Regular exponential families formfinite dimensional linear subspaces of A2(P) and they correspond to finite dimensionalsubspaces formed by their posterior in the dual information space A2(Pprior).The Aitchison norm can identified with mean Fisher information. The closing constant itself is identified with a generalization of the cummulant function and shown to be Kullback Leiblers directed information. Fisher information is the local geometry of the manifold induced by the A2(P) derivative of the Kullback Leibler information and the space A2(P) can therefore be seen as the tangential geometry of statistical inference at the distribution P.The discussion of A2(P) valued random variables, such as estimation functionsor likelihoods, give a further interpretation of Fisher information as the expected squared norm of evidence and a scale free understanding of unbiased reasoningGeologische Vereinigung; Institut d’Estadística de Catalunya; International Association for Mathematical Geology; Patronat de l’Escola Politècnica Superior de la Universitat de Girona; Fundació privada: Girona, Universitat i Futur; Càtedra Lluís Santaló d’Aplicacions de la Matemàtica; Consell Social de la Universitat de Girona; Ministerio de Ciencia i Tecnología

Analyzing shapes as compositions of distances

We propose to analyze shapes as “compositions” of distances in Aitchison geometry asan alternate and complementary tool to classical shape analysis, especially when sizeis non-informative.Shapes are typically described by the location of user-chosen landmarks. Howeverthe shape – considered as invariant under scaling, translation, mirroring and rotation– does not uniquely define the location of landmarks. A simple approach is to usedistances of landmarks instead of the locations of landmarks them self. Distances arepositive numbers defined up to joint scaling, a mathematical structure quite similar tocompositions. The shape fixes only ratios of distances. Perturbations correspond torelative changes of the size of subshapes and of aspect ratios. The power transformincreases the expression of the shape by increasing distance ratios. In analogy to thesubcompositional consistency, results should not depend too much on the choice ofdistances, because different subsets of the pairwise distances of landmarks uniquelydefine the shape.Various compositional analysis tools can be applied to sets of distances directly or afterminor modifications concerning the singularity of the covariance matrix and yield resultswith direct interpretations in terms of shape changes. The remaining problem isthat not all sets of distances correspond to a valid shape. Nevertheless interpolated orpredicted shapes can be backtransformated by multidimensional scaling (when all pairwisedistances are used) or free geodetic adjustment (when sufficiently many distancesare used)Geologische Vereinigung; Institut d’Estadística de Catalunya; International Association for Mathematical Geology; Patronat de l’Escola Politècnica Superior de la Universitat de Girona; Fundació privada: Girona, Universitat i Futur; Càtedra Lluís Santaló d’Aplicacions de la Matemàtica; Consell Social de la Universitat de Girona; Ministerio de Ciencia i Tecnología

A compositional data analysis package for R providing multiple approaches

”compositions” is a new R-package for the analysis of compositional and positive data.It contains four classes corresponding to the four different types of compositional andpositive geometry (including the Aitchison geometry). It provides means for computation,plotting and high-level multivariate statistical analysis in all four geometries.These geometries are treated in an fully analogous way, based on the principle of workingin coordinates, and the object-oriented programming paradigm of R. In this way,called functions automatically select the most appropriate type of analysis as a functionof the geometry. The graphical capabilities include ternary diagrams and tetrahedrons,various compositional plots (boxplots, barplots, piecharts) and extensive graphical toolsfor principal components. Afterwards, ortion and proportion lines, straight lines andellipses in all geometries can be added to plots. The package is accompanied by ahands-on-introduction, documentation for every function, demos of the graphical capabilitiesand plenty of usage examples. It allows direct and parallel computation inall four vector spaces and provides the beginner with a copy-and-paste style of dataanalysis, while letting advanced users keep the functionality and customizability theydemand of R, as well as all necessary tools to add own analysis routines. A completeexample is included in the appendixGeologische Vereinigung; Institut d’Estadística de Catalunya; International Association for Mathematical Geology; Patronat de l’Escola Politècnica Superior de la Universitat de Girona; Fundació privada: Girona, Universitat i Futur; Càtedra Lluís Santaló d’Aplicacions de la Matemàtica; Consell Social de la Universitat de Girona; Ministerio de Ciencia i Tecnología

Mixing compositions and other scales

Theory of compositional data analysis is often focused on the composition only. However in practical applications we often treat a composition together with covariableswith some other scale. This contribution systematically gathers and develop statistical tools for this situation. For instance, for the graphical display of the dependenceof a composition with a categorical variable, a colored set of ternary diagrams mightbe a good idea for a first look at the data, but it will fast hide important aspects ifthe composition has many parts, or it takes extreme values. On the other hand colored scatterplots of ilr components could not be very instructive for the analyst, if theconventional, black-box ilr is used.Thinking on terms of the Euclidean structure of the simplex, we suggest to set upappropriate projections, which on one side show the compositional geometry and on theother side are still comprehensible by a non-expert analyst, readable for all locations andscales of the data. This is e.g. done by defining special balance displays with carefully-selected axes. Following this idea, we need to systematically ask how to display, explore,describe, and test the relation to complementary or explanatory data of categorical, real,ratio or again compositional scales.This contribution shows that it is sufficient to use some basic concepts and very fewadvanced tools from multivariate statistics (principal covariances, multivariate linearmodels, trellis or parallel plots, etc.) to build appropriate procedures for all these combinations of scales. This has some fundamental implications in their software implementation, and how might they be taught to analysts not already experts in multivariateanalysisGeologische Vereinigung; Institut d’Estadística de Catalunya; International Association for Mathematical Geology; Càtedra Lluís Santaló d’Aplicacions de la Matemàtica; Generalitat de Catalunya, Departament d’Innovació, Universitats i Recerca; Ministerio de Educación y Ciencia; Ingenio 2010

News from compositions, the R package

The R-package “compositions”is a tool for advanced compositional analysis. Its basicfunctionality has seen some conceptual improvement, containing now some facilitiesto work with and represent ilr bases built from balances, and an elaborated subsys-tem for dealing with several kinds of irregular data: (rounded or structural) zeroes,incomplete observations and outliers. The general approach to these irregularities isbased on subcompositions: for an irregular datum, one can distinguish a “regular” sub-composition (where all parts are actually observed and the datum behaves typically)and a “problematic” subcomposition (with those unobserved, zero or rounded parts, orelse where the datum shows an erratic or atypical behaviour). Systematic classificationschemes are proposed for both outliers and missing values (including zeros) focusing onthe nature of irregularities in the datum subcomposition(s).To compute statistics with values missing at random and structural zeros, a projectionapproach is implemented: a given datum contributes to the estimation of the desiredparameters only on the subcompositon where it was observed. For data sets withvalues below the detection limit, two different approaches are provided: the well-knownimputation technique, and also the projection approach.To compute statistics in the presence of outliers, robust statistics are adapted to thecharacteristics of compositional data, based on the minimum covariance determinantapproach. The outlier classification is based on four different models of outlier occur-rence and Monte-Carlo-based tests for their characterization. Furthermore the packageprovides special plots helping to understand the nature of outliers in the dataset.Keywords: coda-dendrogram, lost values, MAR, missing data, MCD estimator,robustness, rounded zerosGeologische Vereinigung; Institut d’Estadística de Catalunya; International Association for Mathematical Geology; Càtedra Lluís Santaló d’Aplicacions de la Matemàtica; Generalitat de Catalunya, Departament d’Innovació, Universitats i Recerca; Ministerio de Educación y Ciencia; Ingenio 2010

Resource Model Updating For Compositional Geometallurgical Variables

In the field of mineral resources extraction, one main challenge is to meet production targets in terms of geometallurgical properties. These properties influence the processing of the ore and are often represented in resource modeling by coregionalized variables with a complex relationship between them. Valuable data are available about geometalurgical properties and their interaction with the beneficiation process given sensor technologies during production monitoring. The aim of this research is to update resource models as new observations become available. A popular method for updating is the ensemble Kalman filter. This method relies on Gaussian assumptions and uses a set of realizations of the simulated models to derive sample covariances that can propagate the uncertainty between real observations and simulated ones. Hence, the relationship among variables has a compositional nature, such that updating these models while keeping the compositional constraints is a practical requirement in order to improve the accuracy of the updated models. This paper presents an updating framework for compositional data based on ensemble Kalman filter which allows us to work with compositions that are transformed into a multivariate Gaussian space by log-ratio transformation and flow anamorphosis. This flow anamorphosis, transforms the distribution of the variables to joint normality while reasonably keeping the dependencies between components. Furthermore, the positiveness of those variables, after updating the simulated models, is satisfied. The method is implemented in a bauxite deposit, demonstrating the performance of the proposed approach.Helmholtz-Zentrum Dresden - Rossendorf e. V. (4213