Creating Optimal Conditions for Reproducible Data Analysis in R with ‘Fertile’

The advancement of scientific knowledge increasingly depends on ensuring that data-driven research is reproducible: that two people with the same data obtain the same results. However, while the necessity of reproducibility is clear, there are significant behavioral and technical challenges that impede its widespread implementation and no clear consensus on standards of what constitutes reproducibility in published research. We present fertile, an R package that focuses on a series of common mistakes programmers make while conducting data science projects in R, primarily through the RStudio integrated development environment. fertile operates in two modes: proactively, to prevent reproducibility mistakes from happening in the first place, and retroactively, analyzing code that is already written for potential problems. Furthermore, fertile is designed to educate users on why their mistakes are problematic and how to fix them

Modélisation sémantique des bases de données d'inventaires en cycle de vie

L'analyse des impacts environnementaux de la production de biens et de services est aujourd'hui devenue un enjeu majeur. L'analyse en cycle de vie est la méthode consacrée pour modéliser les impacts environnementaux des activités humaines. L'inventaire en cycle de vie, qui est l'une des étapes de cette méthode, consiste à décomposer les activités économiques en processus interdépendants. Chaque processus a des impacts environnementaux et la composition de ces processus nous donne l'impact cumulé des activités étudiées. Plusieurs entreprises et agences gouvernementales fournissent des bases de données d'inventaires en cycle de vie pour que les experts puissent réutiliser des processus déjà étudiés lors de l'analyse d'un nouveau système. L'audit et la compréhension de ces inventaires nécessite de s'intéresser à un très grand nombre de processus et à leurs relations d'interdépendance. Ces bases de données peuvent comporter plusieurs milliers de processus et des dizaines de milliers de relations de dépendance. Pour les experts qui utilisent les bases de données d'inventaire en cycle de vie, deux problèmes importants sont clairement identifiés : - organiser les processus pour avoir une meilleure compréhensibilité du modèle ; - calculer les impacts d'une modélisation (composition de processus) et, le cas échéant, détecter les raisons de la non convergence du calcul. Dans cette thèse, nous : - mettons en évidence de l'existence de similarités sémantiques entre les processus et leurs relations d'interdépendance et proposons une nouvelle approche pour modéliser les relations d'interdépendance entre les processus d'une base de données d'inventaire. Elle se base sur un étiquetage sémantique des processus à l'aide d'une ontologie et une modélisation multi-niveaux des relations d'interdépendance entre les processus. Nous étudions aussi deux approches déclaratives d'interaction avec ce modèle multi-niveau. - étudions les différentes méthodes de calcul des impacts basées sur des notions classiques d'algèbre linéaire et de théorie des graphes. Nous étudions aussi les conditions de non convergence de ces méthodes en présence de cycle dans le modèle des relations de dépendances. Un prototype implémentant cette approche a montré des résultats probants sur les cas étudiés. Nous avons réalisé une étude de cas de ce prototype sur les processus de production d'électricité aux États-Unis extraits de la base de données d'inventaire en cycle de vie de l'agence environnementale américaine. Ce prototype est à la base d'une application opérationnelle utilisée par l'entreprise.Environmental impact assessment of goods and services is nowadays a major challenge for both economic and ethical reasons. Life Cycle Assessment provides a well accepted methodology for modeling environmental impacts of human activities. This methodology relies on the decomposition of a studied system into interdependent processes in a step called Life Cycle Inventory. Every process has several environmental impacts and the composition of those processes provides the cumulated environmental impact for the studied human activities. Several organizations provide processes databases containing several thousands of processes with their interdependency links that are used by LCA practitioners to do an LCA study. Understanding and audit of those databases requires to analyze a huge amount of processes and their dependency relations. But those databases can contain thousands of processes linked together. We identified two problems that the experts faces using those databases: - organize the processes and their dependency relations to improve the comprehensibility; - calculate the impacts and, if it is not possible, find why it is not feasible. In this thesis, we: - show that there are some semantic similarities between the processes and their dependency relations and propose a new way to model the dependency relations in an inventory database. In our approach, we semantically index the processes using an ontology and we use a multi-layers model of the dependency relations. We also study a declarative approach of this multi-layers approach; - propose a method to calculate the environmental impacts of the processes based on linear algebra and graph theory, and we study the conditions of the feasibility of this calculation when we have a cyclic model. We developed a prototype based on this approach that showed some convincing results on different use cases. We tested our prototype on a case study based on a data set extracted from the National Renewable Energy restricted to the electricity production in the United-States.VILLEURBANNE-DOC'INSA-Bib. elec. (692669901) / SudocSudocFranceF

Dissecting a hot molecular core: The case of G31.41+0.31

We made a detailed observational analysis of a well known hot molecular core lying in the high-mass star-forming region G31.41+0.31. This core is believed to contain deeply embedded massive stars and presents a velocity gradient that has been interpreted either as rotation or as expansion, depending on the authors. Our aim was to shed light on this question and possibly prepare the ground for higher resolution ALMA observations which could directly detect circumstellar disks around the embedded massive stars. Observations at sub-arcsecond resolution were performed with the Submillimeter Array in methyl cyanide, a typical hot molecular core tracer, and 12CO and 13CO, well known outflow tracers. We also obtained sensitive continuum maps at 1.3 mm. Our findings confirm the existence of a sharp velocity gradient across the core, but cannot confirm the existence of a bipolar outflow perpendicular to it. The improved angular resolution and sampling of the uv plane allow us to attain higher quality channel maps of the CH3CN lines with respect to previous studies and thus significantly improve our knowledge of the structure and kinematics of the hot molecular core. While no conclusive argument can rule out any of the two interpretations (rotation or expansion) proposed to explain the velocity gradient observed in the core, in our opinion the observational evidence collected so far indicates the rotating toroid as the most likely scenario. The outflow hypothesis appears less plausible, because the dynamical time scale is too short compared to that needed to form species such as CH3CN, and the mass loss and momentum rates estimated from our measurements appear too high.Comment: Astronomy and Astrophysics, in pres

Atmospheric PSF Interpolation for Weak Lensing in Short Exposure Imaging Data

A main science goal for the Large Synoptic Survey Telescope (LSST) is to measure the cosmic shear signal from weak lensing to extreme accuracy. One difficulty, however, is that with the short exposure time ($\simeq$15 seconds) proposed, the spatial variation of the Point Spread Function (PSF) shapes may be dominated by the atmosphere, in addition to optics errors. While optics errors mainly cause the PSF to vary on angular scales similar or larger than a single CCD sensor, the atmosphere generates stochastic structures on a wide range of angular scales. It thus becomes a challenge to infer the multi-scale, complex atmospheric PSF patterns by interpolating the sparsely sampled stars in the field. In this paper we present a new method, PSFent, for interpolating the PSF shape parameters, based on reconstructing underlying shape parameter maps with a multi-scale maximum entropy algorithm. We demonstrate, using images from the LSST Photon Simulator, the performance of our approach relative to a 5th-order polynomial fit (representing the current standard) and a simple boxcar smoothing technique. Quantitatively, PSFent predicts more accurate PSF models in all scenarios and the residual PSF errors are spatially less correlated. This improvement in PSF interpolation leads to a factor of 3.5 lower systematic errors in the shear power spectrum on scales smaller than $\sim13'$, compared to polynomial fitting. We estimate that with PSFent and for stellar densities greater than $\simeq1/{\rm arcmin}^{2}$, the spurious shear correlation from PSF interpolation, after combining a complete 10-year dataset from LSST, is lower than the corresponding statistical uncertainties on the cosmic shear power spectrum, even under a conservative scenario.Comment: 18 pages,12 figures, accepted by MNRA

A flexible service selection for executing virtual services

[EN] With the adoption of a service-oriented paradigm on the Web, many software services are likely to fulfil similar functional needs for end-users. We propose to aggregate functionally equivalent software services within one single virtual service, that is, to associate a functionality, a graphical user interface (GUI), and a set of selection rules. When an end user invokes such a virtual service through its GUI to answer his/her functional need, the software service that best responds to the end-user s selection policy is selected and executed and the result is then rendered to the end-user through the GUI of the virtual service. A key innovation in this paper is the flexibility of our proposed service selection policy. First, each selection policy can refer to heterogeneous parameters (e.g., service price, end-user location, and QoS). Second, additional parameters can be added to an existing or new policy with little investment. Third, the end users themselves define a selection policy to apply during the selection process, thanks to the GUI element added as part of the virtual service design. This approach was validated though the design, implementation, and testing of an end-to-end architecture, including the implementation of several virtual services and utilizing several software services available today on the Web.This work was partially supported in part by SERVERY (Service Platform for Innovative Communication Environment), a CELTIC project that aims to create a Service Marketplace that bridges the Internet and Telco worlds by merging the flexibility and openness of the former with the trustworthiness and reliability of the latter, enabling effective and profitable cooperation among actors.Laga, N.; Bertin, E.; Crespi, N.; Bedini, I.; Molina Moreno, B.; Zhao, Z. (2013). A flexible service selection for executing virtual services. 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Photometric redshifts for the CFHTLS T0004 Deep and Wide fields

We compute photometric redshifts based on the template-fitting method in the fourth public release of the Canada-France-Hawaii Telescope Legacy Survey. This unique multi-colour catalogue comprises u*,g',r',i',z' photometry in four deep fields of 1 deg2 each and 35 deg2 distributed over three Wide fields. Our photometric redshifts are calibrated with and compared to 16,983 high-quality spectroscopic redshifts from several surveys. We find a dispersion of 0.028 and an outlier rate of 3.5% in the Deep field at i'AB < 24 and a dispersion of 0.036 and an outlier rate of 2.8% in the Wide field at i'AB < 22.5. Beyond i'AB = 22.5 in the Wide field the number of outliers rises from 5% to 10% at i'AB<23 and i'AB<24 respectively. For the Wide sample, we find the systematic redshift bias keeps below 1% to i'AB < 22.5, whereas we find no significant bias in the Deep field. We investigated the effect of tile-to-tile photometric variations and demonstrate that the accuracy of our photometric redshifts is reduced by at most 21%. We separate stars from galaxies using both the size and colour information, reducing the contamination by stars in our catalogues from 50% to 8% at i'AB < 22.5 in fields with the highest stellar density while keeping a complete galaxy sample. Our CFHTLS T0004 photometric redshifts are distributed to the community. Our release include 592,891 (i'AB < 22.5) and 244,701 (i'AB < 24) reliable galaxy photometric redshifts in the Wide and Deep fields, respectively.Comment: 18 pages, 17 figure

Weak lensing from space: first cosmological constraints from three-point shear statistics

We use weak lensing data from the Hubble Space Telescope COSMOS survey to measure the second- and third-moments of the cosmic shear field, estimated from about 450,000 galaxies with average redshift ~ 1.3. We measure two- and three-point shear statistics using a tree-code, dividing the signal in E, B and mixed components. We present a detection of the third-order moment of the aperture mass statistic and verify that the measurement is robust against systematic errors caused by point spread function (PSF) residuals and by the intrinsic alignments between galaxies. The amplitude of the measured three-point cosmic shear signal is in very good agreement with the predictions for a WMAP7 best-fit model, whereas the amplitudes of potential systematics are consistent with zero. We make use of three sets of large Lambda CDM simulations to test the accuracy of the cosmological predictions and to estimate the influence of the cosmology-dependent covariance. We perform a likelihood analysis using the measurement and find that the Omega_m-sigma_8 degeneracy direction is well fitted by the relation: sigma_8 (Omega_m/0.30)^(0.49)=0.78+0.11/-0.26. We present the first measurement of a more generalised three-point shear statistic and find a very good agreement with the WMAP7 best-fit cosmology. The cosmological interpretation of this measurement gives sigma_8 (Omega_m/0.30)^(0.46)=0.69 +0.08/-0.14. Furthermore, the combined likelihood analysis of this measurement with the measurement of the second order moment of the aperture mass improves the accuracy of the cosmological constraints, showing the high potential of this combination of measurements to infer cosmological constraints.Comment: 17 pages, 11 figures. MNRAS submitte

Combined strong and weak lensing analysis of 28 clusters from the Sloan Giant Arcs Survey

We study the mass distribution of a sample of 28 galaxy clusters using strong and weak lensing observations. The clusters are selected via their strong lensing properties as part of the Sloan Giant Arcs Survey (SGAS) from the Sloan Digital Sky Survey (SDSS). Mass modelling of the strong lensing information from the giant arcs is combined with weak lensing measurements from deep Subaru/Suprime-cam images to primarily obtain robust constraints on the concentration parameter and the shape of the mass distribution. We find that the concentration c_vir is a steep function of the mass, c_vir \propto M_vir^-0.59\pm0.12, with the value roughly consistent with the lensing-bias-corrected theoretical expectation for high mass (10^15 h^-1 M_sun) clusters. However, the observationally inferred concentration parameters appear to be much higher at lower masses (10^14 h^-1 M_sun), possibly a consequence of the modification to the inner density profiles provided by baryon cooling. The steep mass-concentration relation is also supported from direct stacking analysis of the tangential shear profiles. In addition, we explore the two-dimensional shape of the projected mass distribution by stacking weak lensing shear maps of individual clusters with prior information on the position angle from strong lens modelling, and find significant evidence for a large mean ellipticity with the best-fit value of e = 0.47 \pm 0.06 for the mass distribution of the stacked sample. We find that the luminous cluster member galaxy distribution traces the overall mass distribution very well, although the distribution of fainter cluster galaxies appears to be more extended than the total mass.Comment: 29 pages, 15+9 figures, 7 tables, accepted for publication in MNRA

Size magnification as a complement to Cosmic Shear

We investigate the extent to which cosmic size magnification may be used to com- plement cosmic shear in weak gravitational lensing surveys, with a view to obtaining high-precision estimates of cosmological parameters. Using simulated galaxy images, we find that size estimation can be an excellent complement, finding that unbiased estimation of the convergence field is possible with galaxies with angular sizes larger than the point-spread function (PSF) and signal-to-noise ratio in excess of 10. The statistical power is similar to, but not quite as good as, cosmic shear, and it is subject to different systematic effects. Application to ground-based data will be challeng- ing, with relatively large empirical corrections required to account for with biases for galaxies which are smaller than the PSF, but for space-based data with 0.1 arcsecond resolution, the size distribution of galaxies brighter than i=24 is ideal for accurate estimation of cosmic size magnification.Comment: 11 pages, 11 figures, accepted by MNRA

Large scale outflows from z ~ 0.7 starburst galaxies identified via ultra-strong MgII quasar absorption lines

(Abridged) Star formation-driven outflows are a critical phenomenon in theoretical treatments of galaxy evolution, despite the limited ability of observations to trace them across cosmological timescales. If the strongest MgII absorption-line systems detected in the spectra of background quasars arise in such outflows, "ultra-strong" MgII (USMgII) absorbers would identify significant numbers of galactic winds over a huge baseline in cosmic time, in a manner independent of the luminous properties of the galaxy. To this end, we present the first detailed imaging and spectroscopic study of the fields of two USMgII absorber systems culled from a statistical absorber catalog, with the goal of understanding the physical processes leading to the large velocity spreads that define such systems. Each field contains two bright emission-line galaxies at similar redshift (dv < 300 km/s) to that of the absorption. Lower-limits on their instantaneous star formation rates (SFR) from the observed OII and Hb line fluxes, and stellar masses from spectral template fitting indicate specific SFRs among the highest for their masses at z~0.7. Additionally, their 4000A break and Balmer absorption strengths imply they have undergone recent (~0.01 - 1 Gyr) starbursts. The concomitant presence of two rare phenomena - starbursts and USMgII absorbers - strongly implies a causal connection. We consider these data and USMgII absorbers in general in the context of various popular models, and conclude that galactic outflows are generally necessary to account for the velocity extent of the absorption. We favour starburst driven outflows over tidally-stripped gas from a major interaction which triggered the starburst as the energy source for the majority of systems. Finally, we discuss the implications of these results and speculate on the overall contribution of such systems to the global SFR density at z~0.7.Comment: 15 pages, 6 figure, accepted for publication by MNRA