Compositional Data Analysis with R

R from http://www.r-project.org/ is ‘GNU S’ – a language and environment for statistical computingand graphics. The environment in which many classical and modern statistical techniques havebeen implemented, but many are supplied as packages. There are 8 standard packages and many moreare 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 isa MixeR package for compositional data analysis that provides support foroperations on compositions: perturbation and power multiplication, subcomposition with or withoutresiduals, 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 ofsubsets 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 simpleand 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

Compositional data and Simpson's paradox

Simpson's paradox, also known as amalgamation or aggregation paradox, appears whendealing with proportions. Proportions are by construction parts of a whole, which canbe interpreted as compositions assuming they only carry relative information. TheAitchison inner product space structure of the simplex, the sample space of compositions, explains the appearance of the paradox, given that amalgamation is a nonlinearoperation within that structure. Here we propose to use balances, which are specificelements of this structure, to analyse situations where the paradox might appear. Withthe proposed approach we obtain that the centre of the tables analysed is a naturalway to compare them, which avoids by construction the possibility of a paradox.Key words: Aitchison geometry, geometric mean, orthogonal projection

A longitudinal study of environmental tobacco smoke exposure in children: parental self reports versus age dependent biomarkers

Background: Awareness of the negative effects of smoking on children's health prompted a decrease in the self-reporting of parental tobacco use in periodic surveys from most industrialized countries. Our aim is to assess changes between ETS exposure at the end of pregnancy and at 4 years of age determined by the parents' self-report and measurement of cotinine in age related biological matrices.Methods: The prospective birth cohort included 487 infants from Barcelona city (Spain). Mothers were asked about maternal and household smoking habit. Cord serum and children's urinary cotinine were analyzed in duplicate using a double antibody radioimmunoassay. Results: At 4 years of age, the median urinary cotinine level in children increased 1.4 or 3.5 times when father or mother smoked, respectively. Cotinine levels in children's urine statistically differentiated children from smoking mothers (Geometric Mean (GM) 19.7 ng/ml; 95% CI 16.83–23.01) and exposed homes (GM 7.1 ng/ml; 95% CI 5.61–8.99) compared with non-exposed homes (GM 4.5 ng/ml; 95% CI 3.71–5.48). Maternal self-reported ETS exposure in homes declined in the four year span between the two time periods from 42.2% to 31.0% (p < 0.01). Nevertheless, most of the children considered non-exposed by their mothers had detectable levels of cotinine above 1 ng/mL in their urine.Conclusion: We concluded that cotinine levels determined in cord blood and urine, respectively, were useful for categorizing the children exposed to smoking and showed that a certain increase in ETS exposure during the 4-year follow-up period occurred.

A nonparametric method for the measurement of size diversity with emphasis on data standardization

The most suitable method for estimation of size diversity is investigated. Size diversity is computed on the basis of the Shannon diversity expression adapted for continuous variables, such as size. It takes the form of an integral involving the probability density function (pdf) of the size of the individuals. Different approaches for the estimation of pdf are compared: parametric methods, assuming that data come from a determinate family of pdfs, and nonparametric methods, where pdf is estimated using some kind of local evaluation. Exponential, generalized Pareto, normal, and log-normal distributions have been used to generate simulated samples using estimated parameters from real samples. Nonparametric methods include discrete computation of data histograms based on size intervals and continuous kernel estimation of pdf. Kernel approach gives accurate estimation of size diversity, whilst parametric methods are only useful when the reference distribution have similar shape to the real one. Special attention is given for data standardization. The division of data by the sample geometric mean is proposedas the most suitable standardization method, which shows additional advantages: the same size diversity value is obtained when using original size or log-transformed data, and size measurements with different dimensionality (longitudes, areas, volumes or biomasses) may be immediately compared with the simple addition of ln k where kis the dimensionality (1, 2, or 3, respectively). Thus, the kernel estimation, after data standardization by division of sample geometric mean, arises as the most reliable and generalizable method of size diversity evaluation

Geometric and long run aspects of Granger causality

This paper extends multivariate Granger causality to take into account the subspacesalong which Granger causality occurs as well as long run Granger causality. The propertiesof these new notions of Granger causality, along with the requisite restrictions, are derivedand extensively studied for a wide variety of time series processes including linear invertibleprocess and VARMA. Using the proposed extensions, the paper demonstrates that: (i) meanreversion in L2 is an instance of long run Granger non-causality, (ii) cointegration is a specialcase of long run Granger non-causality along a subspace, (iii) controllability is a special caseof Granger causality, and finally (iv) linear rational expectations entail (possibly testable)Granger causality restriction along subspaces.

Nanocrystalline M-type hexaferrite powders: preparation, geometric and magnetic propertiess

Co-Ti-Sn-Ge substituted M-type bariumhexaferrite powders with mean grain sizes between about 10 nm and about 1 ¿m and a narrow size distribution were prepared reproducibly by means of a modified glass crystallization method. At annealing temperatures between 560 and 580°C of the amorphous flakes nanocrystalline particles grow. They behave superparamagnetically at room temperature and change into stable magnetic single domains at lower temperatures. The magnetic volume of the powders is considerably less than the geometric one. However, the effective anisotropy fields are larger by a Factor of two to three.

Origin of the neutron skin thickness of 208Pb in nuclear mean-field models

We study whether the neutron skin thickness Δrnp of 208Pb originates from the bulk or from the surface of the nucleon density distributions, according to the mean-field models of nuclear structure, and find that it depends on the stiffness of the nuclear symmetry energy. The bulk contribution to Δrnp arises from an extended sharp radius of neutrons, whereas the surface contribution arises from different widths of the neutron and proton surfaces. Nuclear models where the symmetry energy is stiff, as typical of relativistic models, predict a bulk contribution in Δrnp of 208Pb about twice as large as the surface contribution. In contrast, models with a soft symmetry energy like common nonrelativistic models predict that Δrnp of 208Pb is divided similarly into bulk and surface parts. Indeed, if the symmetry energy is supersoft, the surface contribution becomes dominant. We note that the linear correlation of Δrnp of 208Pb with the density derivative of the nuclear symmetry energy arises from the bulk part of Δrnp. We also note that most models predict a mixed-type (between halo and skin) neutron distribution for 208Pb. Although the halo-type limit is actually found in the models with a supersoft symmetry energy, the skin-type limit is not supported by any mean-field model. Finally, we compute parity-violating electron scattering in the conditions of the 208Pb parity radius experiment (PREX) and obtain a pocket formula for the parity-violating asymmetry in terms of the parameters that characterize the shape of the 208Pb nucleon densities.

Nanocrystalline M-type hexaferrite powders: preparation, geometric and magnetic propertiess

Co-Ti-Sn-Ge substituted M-type bariumhexaferrite powders with mean grain sizes between about 10 nm and about 1 ¿m and a narrow size distribution were prepared reproducibly by means of a modified glass crystallization method. At annealing temperatures between 560 and 580°C of the amorphous flakes nanocrystalline particles grow. They behave superparamagnetically at room temperature and change into stable magnetic single domains at lower temperatures. The magnetic volume of the powders is considerably less than the geometric one. However, the effective anisotropy fields are larger by a Factor of two to three.

Neutron skin of 208Pb, nuclear symmetry energy, and the parity radius experiment

A precise determination of the neutron skin thickness of a heavy nucleus sets a basic constraint on the nuclear symmetry energy (the neutron skin thickness is the difference of the neutron and proton rms radii of the nucleus). The parity radius experiment (PREX) may achieve it by electroweak parity-violating electron scattering (PVES) on 208Pb. We investigate PVES in nuclear mean field approach to allow the accurate extraction of the neutron skin thickness of 208Pb from the parity-violating asymmetry probed in the experiment. We demonstrate a high linear correlation between the parity-violating asymmetry and the neutron skin thickness in successful mean field forces as the best means to constrain the neutron skin of 208Pb from PREX, without assumptions on the neutron density shape. Continuation of the experiment with higher precision in the parity-violating asymmetry is motivated since the present method can support it to constrain the density slope of the nuclear symmetry energy to new accuracy.

Geometric tools to determine the hyperbolicity of limit cycles

"Vegeu el resum a l'inici del document del fitxer adjunt."

The mean dehn functions of Abelian groups

"Vegeu el resum a l'inici del document del fitxer adjunt."

Euclidean geometric invariant of framed knots in manifolds

We present an invariant of a three dimensional manifold with a framed knot in it based on the Reidemeister torsion of an acyclic complex of Euclidean geometric origin. To show its nontriviality, we calculate the invariant for some framed (un)knots in lens spaces. An important feature of our work is that we are not using any nontrivial representation of the manifold fundamental group or knot group.

A computational and geometric approach to phase resetting curves and surfaces

"Vegeu el resum a l'inici del document del fitxer adjunt."

Mean-payoff games and propositional proofs

"Vegeu el resum a l'inici del document del fitxer adjunt."

A geometric mechanism of diffusion: Rigorous verification in a priori unstable Hamiltonian systems

In this paper we consider a representative a priori unstable Hamiltonian system with 2+1/2 degrees of freedom, to which we apply the geometric mechanism for diffusion introduced in the paper Delshams et al., Mem.Amer.Math. Soc. 2006, and generalized in Delshams and Huguet, Nonlinearity 2009, and provide explicit, concrete and easily verifiable conditions for the existence of diffusing orbits. The simplification of the hypotheses allows us to perform explicitly the computations along the proof, which contribute to present in an easily understandable way the geometric mechanism of diffusion. In particular, we fully describe the construction of the scattering map and the combination of two types of dynamics on a normally hyperbolic invariant manifold.