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 and positive 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 working in coordinates, and the object-oriented programming paradigm of R. In this way, called functions automatically select the most appropriate type of analysis as a function of the geometry. The graphical capabilities include ternary diagrams and tetrahedrons, various compositional plots (boxplots, barplots, piecharts) and extensive graphical tools for principal components. Afterwards, ortion and proportion lines, straight lines and ellipses in all geometries can be added to plots. The package is accompanied by a hands-on-introduction, documentation for every function, demos of the graphical capabilities and plenty of usage examples. It allows direct and parallel computation in all four vector spaces and provides the beginner with a copy-and-paste style of data analysis, while letting advanced users keep the functionality and customizability they demand of R, as well as all necessary tools to add own analysis routines. A complete example is included in the appendix

New Features of CoDaPack. An Userfriendly Compositional Data Package

The statistical analysis of compositional data is commonly used in geological studies. As is well-known, compositions should be treated using logratios of parts, which are difficult to use correctly in standard statistical packages. In this paper we describe the new features of our freeware package, named CoDaPack, which implements most of the basic statistical methods suitable for compositional data. An example using real data is presented to illustrate the use of the package

CODAPACK3D. A new version of Compositional Data Package

The statistical analysis of compositional data should be treated using logratios of parts, which are difficult to use correctly in standard statistical packages. For this reason a freeware package, named CoDaPack was created. This software implements most of the basic statistical methods suitable for compositional data. In this paper we describe the new version of the package that now is called CoDaPack3D. It is developed in Visual Basic for applications (associated with Excel©), Visual Basic and Open GL, and it is oriented towards users with a minimum knowledge of computers with the aim at being simple and easy to use. This new version includes new graphical output in 2D and 3D. These outputs could be zoomed and, in 3D, rotated. Also a customization menu is included and outputs could be saved in jpeg format. Also this new version includes an interactive help and all dialog windows have been improved in order to facilitate its use. To use CoDaPack one has to access Excel© and introduce the data in a standard spreadsheet. These should be organized as a matrix where Excel© rows correspond to the observations and columns to the parts. The user executes macros that return numerical or graphical results. There are two kinds of numerical results: new variables and descriptive statistics, and both appear on the same sheet. Graphical output appears in independent windows. In the present version there are 8 menus, with a total of 38 submenus which, after some dialogue, directly call the corresponding macro. The dialogues ask the user to input variables and further parameters needed, as well as where to put these results. The web site http://ima.udg.es/CoDaPack contains this freeware package and only Microsoft Excel© under Microsoft Windows© is required to run the software. Kew words: Compositional data Analysis, Software

News from compositions, the R package

The R-package “compositions”is a tool for advanced compositional analysis. Its basic functionality has seen some conceptual improvement, containing now some facilities to 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 is based 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, or else where the datum shows an erratic or atypical behaviour). Systematic classification schemes are proposed for both outliers and missing values (including zeros) focusing on the nature of irregularities in the datum subcomposition(s). To compute statistics with values missing at random and structural zeros, a projection approach is implemented: a given datum contributes to the estimation of the desired parameters only on the subcompositon where it was observed. For data sets with values below the detection limit, two different approaches are provided: the well-known imputation technique, and also the projection approach. To compute statistics in the presence of outliers, robust statistics are adapted to the characteristics of compositional data, based on the minimum covariance determinant approach. The outlier classification is based on four different models of outlier occur- rence and Monte-Carlo-based tests for their characterization. Furthermore the package provides special plots helping to understand the nature of outliers in the dataset. Keywords: coda-dendrogram, lost values, MAR, missing data, MCD estimator, robustness, rounded zeros

Adaptive integral assessment package for the A2UN@ project

This paper presents a first approach of Evaluation Engine Architecture (EEA) as proposal to support adaptive integral assessment, in the context of a virtual learning environment. The goal of our research is design an evaluation engine tool to assist in the whole assessment process within the A2UN@ project, linking that tool with the other key elements of a learning design (learning task, learning resources and learning support). The teachers would define the relation between knowledge, competencies, activities, resources and type of assessment. Providing this relation is possible obtain more accurate estimations of student's knowledge for adaptive evaluations and future recommendations. The process is supported by usage of educational standards and specifications and for an integral user modelling

An R Library for Compositional Data Analysis in Archaeometry

Compositional data naturally arises from the scientific analysis of the chemical composition of archaeological material such as ceramic and glass artefacts. Data of this type can be explored using a variety of techniques, from standard multivariate methods such as principal components analysis and cluster analysis, to methods based upon the use of log-ratios. The general aim is to identify groups of chemically similar artefacts that could potentially be used to answer questions of provenance. This paper will demonstrate work in progress on the development of a documented library of methods, implemented using the statistical package R, for the analysis of compositional data. R is an open source package that makes available very powerful statistical facilities at no cost. We aim to show how, with the aid of statistical software such as R, traditional exploratory multivariate analysis can easily be used alongside, or in combination with, specialist techniques of compositional data analysis. The library has been developed from a core of basic R functionality, together with purpose-written routines arising from our own research (for example that reported at CoDaWork'03). In addition, we have included other appropriate publicly available techniques and libraries that have been implemented in R by other authors. Available functions range from standard multivariate techniques through to various approaches to log-ratio analysis and zero replacement. We also discuss and demonstrate a small selection of relatively new techniques that have hitherto been little-used in archaeometric applications involving compositional data. The application of the library to the analysis of data arising in archaeometry will be demonstrated; results from different analyses will be compared; and the utility of the various methods discussed

Compositional Data Analysis with R

R from http://www.r-project.org/ is ‘GNU S’ – a language and environment for statistical computing and graphics. The environment in which many classical and modern statistical techniques have been implemented, but many are supplied as packages. There are 8 standard packages and many more are available through the cran family of Internet sites http://cran.r-project.org . We started to develop a library of functions in R to support the analysis of mixtures and our goal is a MixeR package for compositional data analysis that provides support for operations on compositions: perturbation and power multiplication, subcomposition with or without residuals, centering of the data, computing Aitchison’s, Euclidean, Bhattacharyya distances, compositional Kullback-Leibler divergence etc. graphical presentation of compositions in ternary diagrams and tetrahedrons with additional features: barycenter, geometric mean of the data set, the percentiles lines, marking and coloring of subsets of the data set, theirs geometric means, notation of individual data in the set . . . dealing with zeros and missing values in compositional data sets with R procedures for simple and multiplicative replacement strategy, the time series analysis of compositional data. We’ll present the current status of MixeR development and illustrate its use on selected data sets

Descripció de propietats moleculars i activitats biològiques emprant l'energia de repulsió electró-electró

En aquest treball es descriu l'ús de les mesures de semblança molecular quàntica (MSMQ) per a caracteritzar propietats i activitats biològiques moleculars, i definir descriptors emprables per a construir models QSAR i QSPR. L'estudi que es presenta consisteix en la continuació d'un treball recent, on es descrivien relacions entre el paràmetre log P i MSMQ, donant així una alternativa a aquest parimetre hidrofòbic empíric. L'actual contribució presenta una nova mesura, capaç d'estendre l'ús de les MSMQ, que consisteix en l'energia de repulsió electró-electró (Vee). Aquest valor, disponible normalment a partir de programari de química quàntica, considera la molècula com una sola entitat, i no cal recórrer a l'ús de contribucions de fragments. La metodologia s'ha aplicat a cinc tipus diferents de compostos on diferents propietats moleculars i activitats biològiques s'han correlacionat amb Vee com a únic descriptor molecular. En tots els casos estudiats, s'han obtingut correlacions satisfactòries.

La responsabilidad contractual de los organizadores y los detallistas de viajes combinados

Con la entrada en vigor de la Ley 21/1995, de 6 de julio, reguladora de los viajes combinados (LVC) se instaura una nuevo régimen de responsabilidad contractual del organizador y el detallista. Ahora el consumidor de esos viajes no sólo mantiene una relación contractual con el organizador si no también, en su caso, el detallista, cuya actuación deja de tener carácter representativo. Ambos sujetos responderán frente al consumidor "en función de las obligaciones que les correspondan por su ámbito respectivo de gestión del viaje combinado..." (art. 11.1), circunstancia que plantea algunas dificultades en orden a delimitar el alcance de su responsabilidad. Esa misma norma establece la responsabilidad del organizador por los actos de los prestadores de los servicios del viaje utilizados como auxiliares en el cumplimiento contractual. Analizados los sujetos responsables, la presente tesis doctoral estudia los supuestos de incumplimiento del contrato de viaje, las partidas de daños resarcibles y su extensión. El trabajo propone distintos criterios en orden a calcular el valor de los daños por lesión al llamado interés de prestación, los daños corporales, los daños ocasionados por el extravío, destrucción o deterioro de objetos del consumidor, los daños por gastos inútiles y costes de negocios de reemplazo, los daños no patrimoniales y los daños por ganancias dejadas de obtener. Cada una de esas partidas e daños merece un estudio pormenorizado. Así, por ejemplo, se constatan enormes problemas en cuanto a la identificación e indemnización separada de los daños por frustración o pérdida de vacaciones, así como la nesesidad de establecer unas circunstancias a las que los jueces deban acogerse para llevar a cabo su valoración discrecional. La tesis propone que dichas circunstanciasd sean el alcance del incumplimiento del contrato de viaje, las condiciones personales del consumidor, el tipo de vacaciones objeto del viaje contratado y el valor residual de las vacaciones.

Implementation and application of basis set superposition error-correction schemes to the theoretical modeling of weak intermolecular interactions

This thesis deals with the so-called Basis Set Superposition Error (BSSE) from both a methodological and a practical point of view. The purpose of the present thesis is twofold: (a) to contribute step ahead in the correct characterization of weakly bound complexes and, (b) to shed light the understanding of the actual implications of the basis set extension effects in the ab intio calculations and contribute to the BSSE debate. The existing BSSE-correction procedures are deeply analyzed, compared, validated and, if necessary, improved. A new interpretation of the counterpoise (CP) method is used in order to define counterpoise-corrected descriptions of the molecular complexes. This novel point of view allows for a study of the BSSE-effects not only in the interaction energy but also on the potential energy surface and, in general, in any property derived from the molecular energy and its derivatives A program has been developed for the calculation of CP-corrected geometry optimizations and vibrational frequencies, also using several counterpoise schemes for the case of molecular clusters. The method has also been implemented in Gaussian98 revA10 package. The Chemical Hamiltonian Approach (CHA) methodology has been also implemented at the RHF and UHF levels of theory for an arbitrary number interacting systems using an algorithm based on block-diagonal matrices. Along with the methodological development, the effects of the BSSE on the properties of molecular complexes have been discussed in detail. The CP and CHA methodologies are used for the determination of BSSE-corrected molecular complexes properties related to the Potential Energy Surfaces and molecular wavefunction, respectively. First, the behaviour of both BSSE-correction schemes are systematically compared at different levels of theory and basis sets for a number of hydrogen-bonded complexes. The Complete Basis Set (CBS) limit of both uncorrected and CP-corrected molecular properties like stabilization energies and intermolecular distances has also been determined, showing the capital importance of the BSSE correction. Several controversial topics of the BSSE correction are addressed as well. The application of the counterpoise method is applied to internal rotational barriers. The importance of the nuclear relaxation term is also pointed out. The viability of the CP method for dealing with charged complexes and the BSSE effects on the double-well PES blue-shifted hydrogen bonds is also studied in detail. In the case of the molecular clusters the effect of high-order BSSE effects introduced with the hierarchical counterpoise scheme is also determined. The effect of the BSSE on the electron density-related properties is also addressed. The first-order electron density obtained with the CHA/F and CHA/DFT methodologies was used to assess, both graphically and numerically, the redistribution of the charge density upon BSSE-correction. Several tools like the Atoms in Molecules topologycal analysis, density difference maps, Quantum Molecular Similarity, and Chemical Energy Component Analysis were used to deeply analyze, for the first time, the BSSE effects on the electron density of several hydrogen bonded complexes of increasing size. The indirect effect of the BSSE on intermolecular perturbation theory results is also pointed out It is shown that for a BSSE-free SAPT study of hydrogen fluoride clusters, the use of a counterpoise-corrected PES is essential in order to determine the proper molecular geometry to perform the SAPT analysis.