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

Robust Factor Analysis for Compositional Data

Factor analysis as frequent technique for multivariate data inspection is widely used also for compositional data analysis. The usual way is to use a centered logratio (clr) transformation to obtain the random vector y of dimension D. The factor model is then y = Λf + e (1) with the factors f of dimension k < D, the error term e, and the loadings matrix Λ. Using the usual model assumptions (see, e.g., Basilevsky, 1994), the factor analysis model (1) can be written as Cov(y) = ΛΛT + ψ (2) where ψ = Cov(e) has a diagonal form. The diagonal elements of ψ as well as the loadings matrix Λ are estimated from an estimation of Cov(y). Given observed clr transformed data Y as realizations of the random vector y. Outliers or deviations from the idealized model assumptions of factor analysis can severely effect the parameter estimation. As a way out, robust estimation of the covariance matrix of Y will lead to robust estimates of Λ and ψ in (2), see Pison et al. (2003). Well known robust covariance estimators with good statistical properties, like the MCD or the S-estimators (see, e.g. Maronna et al., 2006), rely on a full-rank data matrix Y which is not the case for clr transformed data (see, e.g., Aitchison, 1986). The isometric logratio (ilr) transformation (Egozcue et al., 2003) solves this singularity problem. The data matrix Y is transformed to a matrix Z by using an orthonormal basis of lower dimension. Using the ilr transformed data, a robust covariance matrix C(Z) can be estimated. The result can be back-transformed to the clr space by C(Y ) = V C(Z)V T where the matrix V with orthonormal columns comes from the relation between the clr and the ilr transformation. Now the parameters in the model (2) can be estimated (Basilevsky, 1994) and the results have a direct interpretation since the links to the original variables are still preserved. The above procedure will be applied to data from geochemistry. Our special interest is on comparing the results with those of Reimann et al. (2002) for the Kola project data

Análisis de una iniciativa estudiantil de investigación surgida en Criptogamia, una asignatura optativa de segundo ciclo de Biología = Analysis of a students’ research initiative originating in Cryptogamy, an elective course in the last two years of the Biology degree

Presentamos una experiencia exitosa de aprendizaje que partió de Criptogamia (asignatura optativa de segundo ciclo de Biología), que dio lugar a un proyecto de investigación gestionado por los propios alumnos. La iniciativa se consolidó estableciendo una Asociación de Estudiantes centrada en investigación y divulgación. En poco tiempo, los participantes han presentado comunicaciones científicas, y organizado actividades dirigidas a diversos públicos, dentro y fuera de la comunidad universitaria. Actualmente se plantea una colaboración multidisciplinar con otros organismos de investigación y la extensión de su ámbito de estudio. Abordamos su incidencia en el aprendizaje en varios aspectos: científico (técnicas específicas, rigor, búsqueda de información e interpretación de resultados), comunicativo (estructuración y presentación de la información obtenida, para diversos públicos), y organizativo, incluyendo el trabajo en equipo. Aunque de carácter espontáneo, esta experiencia muestra rasgos evaluables en cuanto a sus posibilidades para otras asignaturas. Analizamos las características y planteamiento de esta optativa, el perfil de sus alumnos, y el contexto universitario que la acoge. Detectamos como factores principales los aspectos participativos de la asignatura, la cohesión del grupo, el carácter voluntario de la implicación, los beneficios percibidos por los estudiantes, y la disponibilidad de recursos humanos (supervisión) y materiales (equipamiento y subvenciones)

Social Networking Technologies: Project Launch

Students taking the 20 credit version of the course (COMP6052) will work in groups of 6 to develop and design a new social networking tool/application/website. The teams will work on their design throughout the semester, and keep a design and development blog that will act as a digital portfolio of their work. At the end of the semester they will also be asked to submit an individual reflective summary that will outline their teams objectives and progress, their part in its progress, and a critical analysis of whether or not they were successful. At the end of the course teams will be asked to pitch their ideas to an interdisciplinary Dragon's Den style panel who will expect them to not only have created something that is technical viable, but will also want to see other economic, social, legal and ethical factors taken into consideration. In this presentation we explain the structure of the group project, what is expected in the blog, and explore some potential ideas to help students understand the scope of the work required. The outcome of the group project does not have to be a fully working piece of software, instead we are looking for a well developed idea that contains enough detail to be convincing to the panel.

Envisioning (starting the project)2: User Stories, Sprint Planning, Risk Assessment

Second in a two part set of lectures on Agile Envisioning. The lectures describe the process of starting up a project. 1) creating a shared understanding amongst the team and customers using Stakeholder Analysis, Personas and User stories 2) Sprint planning and using a burndown chart 3) Risk assessment

Envisioning (starting the project) 1: Stakeholders and Personas

First of a two part set of lectureson Agile Envisioning. The lectures describe the process of starting up a project: building a shared understanding of the customer through Stakeholder Analysis and Personas

Diversity Challenge project

Investigacion sobre las personas incapacitadas y sus necesidades a la hora de entrar a una universidad. Diferencias en los difernetes paises, recomendaciones para lograr suplir las necesidades unicas que ellos necesitan.

Definition of an it project portfolio management methodology for a pharmaceutical company

Con la creciente popularidad de las soluciones de IT como factor clave para aumentar la competitividad y la creación de valor para las empresas, la necesidad de invertir en proyectos de IT se incrementa considerablemente. La limitación de los recursos como un obstáculo para invertir ha obligado a las empresas a buscar metodologías para seleccionar y priorizar proyectos, asegurándose de que las decisiones que se toman son aquellas que van alineadas con las estrategias corporativas para asegurar la creación de valor y la maximización de los beneficios. Esta tesis proporciona los fundamentos para la implementación del Portafolio de dirección de Proyectos de IT (IT PPM) como una metodología eficaz para la gestión de proyectos basados en IT, y una herramienta para proporcionar criterios claros para los directores ejecutivos para la toma de decisiones. El documento proporciona la información acerca de cómo implementar el IT PPM en siete pasos, el análisis de los procesos y las funciones necesarias para su ejecución exitosa. Además, proporciona diferentes métodos y criterios para la selección y priorización de proyectos. Después de la parte teórica donde se describe el IT PPM, la tesis aporta un análisis del estudio de caso de una empresa farmacéutica. La empresa ya cuenta con un departamento de gestión de proyectos, pero se encontró la necesidad de implementar el IT PPM debido a su amplia cobertura de procesos End-to-End en Proyectos de IT, y la manera de asegurar la maximización de los beneficios. Con la investigación teórica y el análisis del estudio de caso, la tesis concluye con una definición práctica de un modelo aproximado IT PPM como una recomendación para su implementación en el Departamento de Gestión de Proyectos.

A qualitative analysis of immigrant population health practices in the Girona Healthcare Region

The research we present here forms part of a two-phase project - one quantitative and the other qualitative - assessing the use of primary health care services. This paper presents the qualitative phase of said research, which is aimed at ascertaining the needs, beliefs, barriers to access and health practices of the immigrant population in comparison with the native population, as well as the perceptions of healthcare professionals. Moroccan and sub-Saharan were the immigrants to who the qualitative phase was specifically addressed. The aims of this paper are as follows: to analyse any possible implications of family organisation in the health practices of the immigrant population; to ascertain social practices relating to illness; to understand the significances of sexual and reproductive health practices; and to ascertain the ideas and perceptions of immigrants, local people and professionals regarding health and the health system. Methods: qualitative research based on discursive analysis. Data gathering techniques consisted of discussion groups with health system users and semi-structured individual interviews with healthcare professionals. The sample was taken from the Basic Healthcare Areas of Salt and Banyoles (belonging to the Girona Healthcare Region), the discussion groups being comprised of (a) 6 immigrant Moroccan women, (b) 7 immigrant sub-Saharan African women and (c) 6 immigrant and native population men (2 native men, 2 Moroccan men and 2 sub-Saharan men); and the semi-structured interviews being conducted with the following healthcare professionals: (a) 3 gynaecologists, (b) 3 nurses and 1 administrative staff. Results: use of the healthcare system is linked to the perception of not being well, knowledge of the healthcare system, length of time resident in Spain and interiorization of traditional Western medicine as a cure mechanism. The divergences found among the groups of immigrants, local people and healthcare professionals with regard to healthcare education, use of the healthcare service, sexual and reproductive healthcare and reticence with regard to being attended by healthcare personnel of the opposite sex demonstrate a need to work with the immigrant population as a heterogeneous group. Conclusions: the results we have obtained support the idea that feeling unwell is a psycho-social process, as it takes place within a specific socio-cultural situation and spans a range of beliefs, perceptions and ideas regarding symptomology and how to treat it

El Fotomuntatge arquitectònic. El cas de Mies Van der Rohe

El treball realitzat vol ser un anàlisi exhaustiu de l'efecte causat per l'aparició de la fotografia en la representació de l'arquitectura, la seva introducció en les presentacions dels projectes i l'ús del fotomuntatge. Amb el canvi de segle, del dinou al vint, la fotografia ja va començar a entrar en les diferents disciplines artístiques inclosa l'arquitectura, de tal manera que amb l'aparició de les avantguardes artístiques els moviments arquitectònics moderns també es van mostrar reaccionaris i van incloure, a part de nous conceptes arquitectònics, noves maneres de presentar-les, la qual cosa els va acostar a les propostes pictòriques i conseqüentment a la introducció de la fotografia en el seu procés de treball i de presentació.

The Representation of the Feminine in the Portuguese Press : A Content Analysis of the Diário de Notícias Newspaper

This is a brief report of a research project, coordinated by me and funded by the Portuguese Government. It studies ‘The Representation of the Feminine in the Portuguese Press’ (POCI/COM 55780/2004), and works on the content analysis of discourse on the feminine in various Portuguese newspapers, covering the time span of February 1st till April 30th 2006. The paper is divided into two parts: in the first part, I will briefly discuss the typology used to code the text units of selected articles; in the second part, I will explore the most expressive percentages of the first two weeks of February for the content analysis of the Diário de Notícias newspaper. These percentages were obtained with the NVivo 6 qualitative data treatment software programme.

Reabilitação de edifícios habitacionais com valor patrimonial : o caso do centro histórico de Guimarães

A presente dissertação centra-se no tema “reabilitação de edifícios habitacionais com valor patrimonial – o caso do centro histórico de Guimarães“ Com o passar dos anos tem-se feito, cada vez mais, um esforço para tentar combater as áreas degradadas das cidades e colmatar lacunas referentes às ações tomadas nesse sentido. É necessária a intervenção dos Arquitetos que, através dos seus conhecimentos e poderes, têm a obrigação de manter a história da Arquitetura intacta no tempo. Esta dissertação centra-se em analisar algumas questões inerentes ligadas á reabilitação de edifícios habitacionais, declarando possíveis respostas. As questões vão desde perceber como é que um espaço reabilitado pode ser tão adequado como um espaço pensado de raiz até à questão da utilização de materiais, passando pelo tipo de relacionamento entre o arquiteto e o proprietário, e como os dois protagonistas podem fazer valer as suas ideias em simultâneo. Este trabalho pretende, então, transmitir a importância da reabilitação e preservação dos centros históricos, mostrando que com a reabilitação é possível a sua conservação. Para uma melhor compreensão do tema selecionado, Guimarães apresenta-se como uma cidade que vai ao encontro de todos os pontos referidos até este momento, sendo o seu centro histórico um exemplo de requalificação e conseguindo, com uma metodologia bem determinada, manter todas as origens da cidade, no qual são utilizadas técnicas e materiais tradicionais de construção. A dissertação termina com a análise de cada projeto escolhido para estudo.

A general-method for tracking analysis and its application to meteorological data

Recent interest in the validation of general circulation models (GCMs) has been devoted to objective methods. A small number of authors have used the direct synoptic identification of phenomena together with a statistical analysis to perform the objective comparison between various datasets. This paper describes a general method for performing the synoptic identification of phenomena that can be used for an objective analysis of atmospheric, or oceanographic, datasets obtained from numerical models and remote sensing. Methods usually associated with image processing have been used to segment the scene and to identify suitable feature points to represent the phenomena of interest. This is performed for each time level. A technique from dynamic scene analysis is then used to link the feature points to form trajectories. The method is fully automatic and should be applicable to a wide range of geophysical fields. An example will be shown of results obtained from this method using data obtained from a run of the Universities Global Atmospheric Modelling Project GCM.

Running Climate Models On The NERC Cluster Grid Using G-Rex

Compute grids are used widely in many areas of environmental science, but there has been limited uptake of grid computing by the climate modelling community, partly because the characteristics of many climate models make them difficult to use with popular grid middleware systems. In particular, climate models usually produce large volumes of output data, and running them usually involves complicated workflows implemented as shell scripts. For example, NEMO (Smith et al. 2008) is a state-of-the-art ocean model that is used currently for operational ocean forecasting in France, and will soon be used in the UK for both ocean forecasting and climate modelling. On a typical modern cluster, a particular one year global ocean simulation at 1-degree resolution takes about three hours when running on 40 processors, and produces roughly 20 GB of output as 50000 separate files. 50-year simulations are common, during which the model is resubmitted as a new job after each year. Running NEMO relies on a set of complicated shell scripts and command utilities for data pre-processing and post-processing prior to job resubmission. Grid Remote Execution (G-Rex) is a pure Java grid middleware system that allows scientific applications to be deployed as Web services on remote computer systems, and then launched and controlled as if they are running on the user's own computer. Although G-Rex is general purpose middleware it has two key features that make it particularly suitable for remote execution of climate models: (1) Output from the model is transferred back to the user while the run is in progress to prevent it from accumulating on the remote system and to allow the user to monitor the model; (2) The client component is a command-line program that can easily be incorporated into existing model work-flow scripts. G-Rex has a REST (Fielding, 2000) architectural style, which allows client programs to be very simple and lightweight and allows users to interact with model runs using only a basic HTTP client (such as a Web browser or the curl utility) if they wish. This design also allows for new client interfaces to be developed in other programming languages with relatively little effort. The G-Rex server is a standard Web application that runs inside a servlet container such as Apache Tomcat and is therefore easy to install and maintain by system administrators. G-Rex is employed as the middleware for the NERC1 Cluster Grid, a small grid of HPC2 clusters belonging to collaborating NERC research institutes. Currently the NEMO (Smith et al. 2008) and POLCOMS (Holt et al, 2008) ocean models are installed, and there are plans to install the Hadley Centre’s HadCM3 model for use in the decadal climate prediction project GCEP (Haines et al., 2008). The science projects involving NEMO on the Grid have a particular focus on data assimilation (Smith et al. 2008), a technique that involves constraining model simulations with observations. The POLCOMS model will play an important part in the GCOMS project (Holt et al, 2008), which aims to simulate the world’s coastal oceans. A typical use of G-Rex by a scientist to run a climate model on the NERC Cluster Grid proceeds as follows :(1) The scientist prepares input files on his or her local machine. (2) Using information provided by the Grid’s Ganglia3 monitoring system, the scientist selects an appropriate compute resource. (3) The scientist runs the relevant workflow script on his or her local machine. This is unmodified except that calls to run the model (e.g. with “mpirun”) are simply replaced with calls to "GRexRun" (4) The G-Rex middleware automatically handles the uploading of input files to the remote resource, and the downloading of output files back to the user, including their deletion from the remote system, during the run. (5) The scientist monitors the output files, using familiar analysis and visualization tools on his or her own local machine. G-Rex is well suited to climate modelling because it addresses many of the middleware usability issues that have led to limited uptake of grid computing by climate scientists. It is a lightweight, low-impact and easy-to-install solution that is currently designed for use in relatively small grids such as the NERC Cluster Grid. A current topic of research is the use of G-Rex as an easy-to-use front-end to larger-scale Grid resources such as the UK National Grid service.

Dispersion Experiments in Central London: The 2007 DAPPLE project

In the event of a release of toxic gas in the center of London, the emergency services would need to determine quickly the extent of the area contaminated. The transport of pollutants by turbulent flow within the complex street and building architecture of cities is not straightforward, and we might wonder whether it is at all possible to make a scientifically-reasoned decision. Here we describe recent progress from a major UK project, ‘Dispersion of Air Pollution and its Penetration into the Local Environment’ (DAPPLE, www.dapple.org.uk). In DAPPLE, we focus on the movement of airborne pollutants in cities by developing a greater understanding of atmospheric flow and dispersion within urban street networks. In particular, we carried out full-scale dispersion experiments in central London (UK) during 2003, 2004, 2007, and 2008 to address the extent of the dispersion of tracers following their release at street level. These measurements complemented previous studies because (i) our focus was on dispersion within the first kilometer from the source, when most of the material was expected to remain within the street network rather than being mixed into the boundary layer aloft, (ii) measurements were made under a wide variety of meteorological conditions, and (iii) central London represents a European, rather than North American, city geometry. Interpretation of the results from the full-scale experiments was supported by extensive numerical and wind tunnel modeling, which allowed more detailed analysis under idealized and controlled conditions. In this article, we review the full-scale DAPPLE methodologies and show early results from the analysis of the 2007 field campaign data.