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

A Log-linear model of grain size influence on the geochemistry of sediments

Sediment composition is mainly controlled by the nature of the source rock(s), and chemical (weathering) and physical processes (mechanical crushing, abrasion, hydrodynamic sorting) during alteration and transport. Although the factors controlling these processes are conceptually well understood, detailed quantification of compositional changes induced by a single process are rare, as are examples where the effects of several processes can be distinguished. The present study was designed to characterize the role of mechanical crushing and sorting in the absence of chemical weathering. Twenty sediment samples were taken from Alpine glaciers that erode almost pure granitoid lithologies. For each sample, 11 grain-size fractions from granules to clay (ø grades <-1 to >9) were separated, and each fraction was analysed for its chemical composition. The presence of clear steps in the box-plots of all parts (in adequate ilr and clr scales) against ø is assumed to be explained by typical crystal size ranges for the relevant mineral phases. These scatter plots and the biplot suggest a splitting of the full grain size range into three groups: coarser than ø=4 (comparatively rich in SiO2, Na2O, K2O, Al2O3, and dominated by “felsic” minerals like quartz and feldspar), finer than ø=8 (comparatively rich in TiO2, MnO, MgO, Fe2O3, mostly related to “mafic” sheet silicates like biotite and chlorite), and intermediate grains sizes (4≤ø <8; comparatively rich in P2O5 and CaO, related to apatite, some feldspar). To further test the absence of chemical weathering, the observed compositions were regressed against three explanatory variables: a trend on grain size in ø scale, a step function for ø≥4, and another for ø≥8. The original hypothesis was that the trend could be identified with weathering effects, whereas each step function would highlight those minerals with biggest characteristic size at its lower end. Results suggest that this assumption is reasonable for the step function, but that besides weathering some other factors (different mechanical behavior of minerals) have also an important contribution to the trend. Key words: sediment, geochemistry, grain size, regression, step function

An alternative method for dating unknown tephras based on a segmented regression model

In CoDaWork’05, we presented an application of discriminant function analysis (DFA) to 4 different compositional datasets and modelled the first canonical variable using a segmented regression model solely based on an observation about the scatter plots. In this paper, multiple linear regressions are applied to different datasets to confirm the validity of our proposed model. In addition to dating the unknown tephras by calibration as discussed previously, another method of mapping the unknown tephras into samples of the reference set or missing samples in between consecutive reference samples is proposed. The application of these methodologies is demonstrated with both simulated and real datasets. This new proposed methodology provides an alternative, more acceptable approach for geologists as their focus is on mapping the unknown tephra with relevant eruptive events rather than estimating the age of unknown tephra. Kew words: Tephrochronology; Segmented regression

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 covariables with some other scale. This contribution systematically gathers and develop statistical tools for this situation. For instance, for the graphical display of the dependence of a composition with a categorical variable, a colored set of ternary diagrams might be a good idea for a first look at the data, but it will fast hide important aspects if the 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 the conventional, black-box ilr is used. Thinking on terms of the Euclidean structure of the simplex, we suggest to set up appropriate projections, which on one side show the compositional geometry and on the other side are still comprehensible by a non-expert analyst, readable for all locations and scales 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 few advanced tools from multivariate statistics (principal covariances, multivariate linear models, 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 multivariate analysis

Correlacion entre bilirrubinometría transcutanea y bilirrubina serica en neonatos a termino o cercanos al termino con ictericia

La ictericia es causa frecuente de hospitalización en neonatos. El objetivo principal fue establecer la correlación entre bilirrubinometría transcutánea y bilirrubina sérica, y su utilidad para identificar requerimiento de fototerapia. Materiales y métodos: Es un estudio descriptivo de correlación. Incluyó neonatos con realización de bilirrubinometría transcutánea y bilirrubina sérica. Se calculan índices de correlación de Pearson para el tórax y la frente. La variabilidad de las diferencias entre niveles transcutáneos y bilirrubina séricas, se correlacionan, mediante diagrama de Bland-Altman. Se obtienen mediciones de desempeño de la prueba, con sensibilidad y especificidad. Resultados: Se incluyeron 88 Neonatos, con 112 bilirrubinometrías transcutáneas, (mediana en tórax: 6,0 mg/dl y en frente: 5,9 mg/dl). Se tomaron 95 muestras de bilirrubina sérica, (mediana: 7,2 mg/dl). Los índices de correlación de Pearson fueron 0.83 (tórax) y 0.93 (frente). Utilizando puntos de corte establecidos, para determinar la necesidad de fototerapia, se obtuvieron, sensibilidad del 93 % y especificidad del 86 % (tórax), y sensibilidad del 94% y especificidad del 83 % (frente). Utilizando percentiles 75 del gráfico de Buthani, se obtuvieron sensibilidad del 83% y Especificidad del 98% para la bilirrubinometría transcutánea. Discusión: Las mediciones transcutáneas se correlacionaron bien con las sanguíneas. Las sensibilidades obtenidas fueron satisfactorias. Conclusión: Las mediciones transcutáneas, hubieran detectado la mayoría de infantes que requirieron fototerapia, confirmando la utilidad como método no invasivo en la práctica clínica.

Introduction to 'Surfer'

'Surfer' is a computer package used to produce contour plots. Its marine applications therefore include production of bathymetric maps from measurements of depth, as well as contour plots of how oceanographic parameters vary in space and time in the water column.

Laboratory on Matlab

Considers function handles, matrix manipulation, 3D plots and programming

Análisis del impacto del tamaño de los activos en la cuenta de resultados mediante la utilización de espacios de fase y análisis de recurrencia

Los resultados financieros de las organizaciones son objeto de estudio y análisis permanente, predecir sus comportamientos es una tarea permanente de empresarios, inversionistas, analistas y académicos. En el presente trabajo se explora el impacto del tamaño de los activos (valor total de los activos) en la cuenta de resultados operativos y netos, analizando inicialmente la relación entre dichas variables con indicadores tradicionales del análisis financiero como es el caso de la rentabilidad operativa y neta y con elementos de estadística descriptiva que permiten calificar los datos utilizados como lineales o no lineales. Descubriendo posteriormente que los resultados financieros de las empresas vigiladas por la Superintendencia de Sociedades para el año 2012, tienen un comportamiento no lineal, de esta manera se procede a analizar la relación de los activos y los resultados con la utilización de espacios de fase y análisis de recurrencia, herramientas útiles para sistemas caóticos y complejos. Para el desarrollo de la investigación y la revisión de la relación entre las variables de activos y resultados financieros se tomó como fuente de información los reportes financieros del cierre del año 2012 de la Superintendencia de Sociedades (Superintendencia de Sociedades, 2012).

La transformación del sistema de partidos políticos en Turquía entre 2001 y 2014

El propósito de esta investigación es analizar los cambios que trajo consigo la llegada del Partido de la Justicia y Desarrollo al poder (AKP), en Turquía. Este partido se presentó como conservador moderado y democrático y esto le permitió llegar al poder y mantenerlo desde 2001 hasta la actualidad, pues recibió el apoyo de diversos grupos políticos. La noción general que dio el AKP a la opinión pública era que un partido conservador estaba iniciando un proceso democrático real en Turquía. Sin embargo, el líder del AKP y sus seguidores viraron, desde el 2007, hacia el islamismo. Usando la teoría del clivaje social, propuesta Stein Rokkan y Seymour Lipset, se intenta demostrar que los cambios realizados por el AKP fueron una estrategia para blindarse en el poder, pero el sistema de partidos mantuvo la lógica de los clivajes tradicionales y el clivaje islamismo-kemalismo se consolidó como el principal.

Tratamiento de Artritis reumatoide con antagonistas del factor de necrosis tumoral alfa y su asociación con el desarrollo de melanoma cutáneo: revisión sistemática de la literatura y meta-análisis.

Introducción: El tratamiento con antagonistas del factor de necrosis tumoral alfa (anti TNF) ha impactado el pronóstico y la calidad de vida de los pacientes con artritis reumatoide (AR) positivamente, sin embargo, se interroga un incremento en el riesgo de desarrollar melanoma. Objetivo: Conocer la asociación entre el uso de anti TNF y el desarrollo de melanoma maligno en pacientes con AR. Metodología: Se realizó una búsqueda sistemática en MEDLINE, EMBASE, COCHRANE LIBRARY y LILACS para ensayos clínicos, estudios observacionales, revisiones y meta-análisis en pacientes adultos con diagnóstico de AR y manejo con anti TNF (Certolizumab pegol, Adalimumab, Etanercept, Infliximab y Golimumab). Resultados: 37 estudios clínicos cumplieron los criterios de inclusión para el meta-análisis, con una población de 16567 pacientes. El análisis de heterogeneidad no fue significativo (p=1), no se encontró diferencia en el riesgo entre los grupos comparados DR -0.00 (IC 95% -0.001; -0.001). Un análisis adicional de los estudios en los que se reportó al menos 1 caso de melanoma (4222 pacientes) tampoco mostró diferencia en el riesgo DR -0.00 (IC 95% -0.004 ; -0.003). Conclusión: En la evidencia disponible a la fecha no encontramos asociación significativa entre el tratamiento con anti TNF en pacientes con diagnóstico de AR y el desarrollo de melanoma cutáneo.

La pelota no se mancha: Un estudio histórico sobre el desarrollo y la política en FIFA

Esta investigación se centra en la Fédération Internationale de Football Association (FIFA) como organización política. Intenta responder dos interrogantes primordiales: 1) ¿cómo la FIFA ha constituido el poder que tiene actualmente y, así, hacerse del monopolio indiscutido del fútbol? Y 2) ¿cómo ha cambiado en el tiempo la política interna de FIFA y su vínculo con la política internacional? Para lograr esto, se realiza un estudio histórico, basado principalmente en documentos, que intenta caracterizar y analizar los cambios de la organización en el tiempo. Se enfatizan las últimas dos presidencias de FIFA, de João Havelange y Joseph Blatter, como casos de estudio.

Distinct Unfolding and Refolding Pathways of Ribonuclease A Revealed by Heating and Cooling Temperature Jumps

Heating and cooling temperature jumps (T-jumps) were performed using a newly developed technique to trigger unfolding and refolding of wild-type ribonuclease A and a tryptophan-containing variant (Y115W). From the linear Arrhenius plots of the microscopic folding and unfolding rate constants, activation enthalpy (ΔH#), and activation entropy (ΔS#) were determined to characterize the kinetic transition states (TS) for the unfolding and refolding reactions. The single TS of the wild-type protein was split into three for the Y115W variant. Two of these transition states, TS1 and TS2, characterize a slow kinetic phase, and one, TS3, a fast phase. Heating T-jumps induced protein unfolding via TS2 and TS3; cooling T-jumps induced refolding via TS1 and TS3. The observed speed of the fast phase increased at lower temperature, due to a strongly negative ΔH# of the folding-rate constant. The results are consistent with a path-dependent protein folding/unfolding mechanism. TS1 and TS2 are likely to reflect X-Pro114 isomerization in the folded and unfolded protein, respectively, and TS3 the local conformational change of the β-hairpin comprising Trp115. A very fast protein folding/unfolding phase appears to precede both processes. The path dependence of the observed kinetics is suggestive of a rugged energy protein folding funne

Vesper Sparrows and Western Meadowlarks Show a Mixed Response to Cattle Grazing in the Intermountain Region of British Columbia

Livestock grazing in the shortgrass steppe of the Intermountain region of British Columbia is predicted to have significant effects on grassland habitats and their associated ground-nesting bird communities. We tested whether grazed and ungrazed sites could be discriminated on the basis of their vegetation communities, whether the abundance of two ground-nesting bird species, Vesper Sparrow (Pooecetes gramineus) and Western Meadowlark (Sturnella neglecta), differed between grazed and ungrazed sites, and whether vegetation variables found to differ between grazed and ungrazed plots could be used to predict the abundance of the two bird species at a fine scale. Grazed sites were easily distinguishable from a site that had been ungrazed for >30 years based on the structure and composition of their vegetation communities. However, more detailed grazing categories could not be distinguished on the basis of vegetation characteristics. Despite the existence of grazing effects on vegetation structure and composition, we found no consistent differences in abundance of Vesper Sparrows and Western Meadowlarks between the grazed and ungrazed sites. However, there was weak evidence that the abundance of both species was higher at fine-scale plots (100 m radius point count station) with less bare ground and taller vegetation. Bare ground cover was lower on grazed plots, but vegetation was taller on ungrazed plots. Combined, our results suggest that low intensity grazing leads to grassland habitat change with both negative and positive effects on Vesper Sparrows and Western Meadowlarks, resulting in no net change in their broad-scale abundance.

Patch Scale Nest-Site Selection by Marbled Murrelets (Brachyramphus marmoratus)

The Marbled Murrelet (Brachyramphus marmoratus) is a threatened alcid that nests almost exclusively in old-growth forests along the Pacific coast of North America. Nesting habitat has significant economic importance. Murrelet nests are extremely difficult and costly to find, which adds uncertainty to management and conservation planning. Models based on air photo interpretation of forest cover maps or assessments by low-level helicopter flights are currently used to rank presumed Marbled Murrelet nesting habitat quality in British Columbia. These rankings are assumed to correlate with nest usage and murrelet breeding productivity. Our goal was to find the models that best predict Marbled Murrelet nesting habitat in the ground-accessible portion of the two regions studied. We generated Resource Selection Functions (RSF) using logistic regression models of ground-based forest stand variables gathered at plots around 64 nests, located using radio-telemetry, versus 82 random habitat plots. The RSF scores are proportional to the probability of nests occurring in a forest patch. The best models differed somewhat between the two regions, but include both ground variables at the patch scale (0.2-2.0 ha), such as platform tree density, height and trunk diameter of canopy trees and canopy complexity, and landscape scale variables such as elevation, aspect, and slope. Collecting ground-based habitat selection data would not be cost-effective for widespread use in forestry management; air photo interpretation and low-level aerial surveys are much more efficient methods for ranking habitat suitability on a landscape scale. This study provides one method for ground-truthing the remote methods, an essential step made possible using the numerical RSF scores generated herein.

Numerical Response of Breeding Birds Following Experimental Selection Harvesting in Northern Hardwood Forests

Silvicultural treatments have been shown to alter the composition of species assemblages in numerous taxa. However, the intensity and persistence of these effects have rarely been documented. We used a before-after, control-impact (BACI) paired design, i.e., five pairs of 25-ha study plots, 1-control and 1-treated plot, to quantify changes in the density of eight forest bird species in response to selection harvesting over six breeding seasons, one year pre- and five years postharvest. Focal species included mature forest associates, i.e., Northern Parula (Setophaga americana) and Black-throated Green Warbler (Setophaga virens), forest generalists, i.e., Yellow-bellied Sapsucker (Sphyrapicus varius) and Swainson’s Thrush (Catharus ustulatus), early-seral specialists, i.e., Mourning Warbler (Geothlypis philadelphia) and Chestnut-sided Warbler (Setophaga pensylvanica), species associated with shrubby forest gaps, i.e., Black-throated Blue Warbler (Setophaga caerulescens), and mid-seral species, i.e., American Redstart (Setophaga ruticilla). As predicted, we found a negative numerical response to the treatment in the Black-throated Green Warbler, no treatment effect in the Yellow-bellied Sapsucker, and a positive treatment effect in early-seral specialists. We only detected a year effect in the Northern Parula and the American Redstart. There was evidence for a positive treatment effect on the Swainson’s Thrush when the regeneration started to reach the pole stage, i.e., fifth year postharvest. These findings suggest that selection harvesting has the potential to maintain diverse avian assemblages while allowing sustainable management of timber supply, but future studies should determine whether mature-forest associates can sustain second- and third-entry selection harvest treatments.