The Overlooked Potential of Generalized Linear Models in Astronomy - I: Binomial Regression

Revealing hidden patterns in astronomical data is often the path to fundamental scientific breakthroughs; meanwhile the complexity of scientific inquiry increases as more subtle relationships are sought. Contemporary data analysis problems often elude the capabilities of classical statistical techniques, suggesting the use of cutting edge statistical methods. In this light, astronomers have overlooked a whole family of statistical techniques for exploratory data analysis and robust regression, the so-called Generalized Linear Models (GLMs). In this paper -- the first in a series aimed at illustrating the power of these methods in astronomical applications -- we elucidate the potential of a particular class of GLMs for handling binary/binomial data, the so-called logit and probit regression techniques, from both a maximum likelihood and a Bayesian perspective. As a case in point, we present the use of these GLMs to explore the conditions of star formation activity and metal enrichment in primordial minihaloes from cosmological hydro-simulations including detailed chemistry, gas physics, and stellar feedback. We predict that for a dark mini-halo with metallicity $\approx 1.3 \times 10^{-4} Z_{\bigodot}$, an increase of $1.2 \times 10^{-2}$ in the gas molecular fraction, increases the probability of star formation occurrence by a factor of 75%. Finally, we highlight the use of receiver operating characteristic curves as a diagnostic for binary classifiers, and ultimately we use these to demonstrate the competitive predictive performance of GLMs against the popular technique of artificial neural networks.Comment: 20 pages, 10 figures, 3 tables, accepted for publication in Astronomy and Computin

Efficient Forward Simulation of Fisher-Wright Populations with Stochastic Population Size and Neutral Single Step Mutations in Haplotypes

In both population genetics and forensic genetics it is important to know how haplotypes are distributed in a population. Simulation of population dynamics helps facilitating research on the distribution of haplotypes. In forensic genetics, the haplotypes can for example consist of lineage markers such as short tandem repeat loci on the Y chromosome (Y-STR). A dominating model for describing population dynamics is the simple, yet powerful, Fisher-Wright model. We describe an efficient algorithm for exact forward simulation of exact Fisher-Wright populations (and not approximative such as the coalescent model). The efficiency comes from convenient data structures by changing the traditional view from individuals to haplotypes. The algorithm is implemented in the open-source R package 'fwsim' and is able to simulate very large populations. We focus on a haploid model and assume stochastic population size with flexible growth specification, no selection, a neutral single step mutation process, and self-reproducing individuals. These assumptions make the algorithm ideal for studying lineage markers such as Y-STR.Comment: 17 pages, 6 figure

Viriato: a Fourier-Hermite spectral code for strongly magnetised fluid-kinetic plasma dynamics

We report on the algorithms and numerical methods used in Viriato, a novel fluid-kinetic code that solves two distinct sets of equations: (i) the Kinetic Reduced Electron Heating Model (KREHM) equations [Zocco & Schekochihin, Phys. Plasmas 18, 102309 (2011)] (which reduce to the standard Reduced-MHD equations in the appropriate limit) and (ii) the kinetic reduced MHD (KRMHD) equations [Schekochihin et al., Astrophys. J. Suppl. 182:310 (2009)]. Two main applications of these equations are magnetised (Alfvenic) plasma turbulence and magnetic reconnection. Viriato uses operator splitting (Strang or Godunov) to separate the dynamics parallel and perpendicular to the ambient magnetic field (assumed strong). Along the magnetic field, Viriato allows for either a second-order accurate MacCormack method or, for higher accuracy, a spectral-like scheme composed of the combination of a total variation diminishing (TVD) third order Runge-Kutta method for the time derivative with a 7th order upwind scheme for the fluxes. Perpendicular to the field Viriato is pseudo-spectral, and the time integration is performed by means of an iterative predictor-corrector scheme. In addition, a distinctive feature of Viriato is its spectral representation of the parallel velocity-space dependence, achieved by means of a Hermite representation of the perturbed distribution function. A series of linear and nonlinear benchmarks and tests are presented, including a detailed analysis of 2D and 3D Orszag-Tang-type decaying turbulence, both in fluid and kinetic regimes.Comment: 42 pages, 15 figures, submitted to J. Comp. Phy

Does organic school food service provide more healthy eating environments than their non organic counterparts?

Organic food strategies are increasingly developing within European school food services at the same time as these services are being involved in measures aiming at promoting healthy eating at school and counteracting obesity. Schools have an important role to play in teaching children fundamental life skills, including good food habits according to a number of authoritative policy papers from Council of Europe, the WHO and the EU platform. Although there are great national differences, European school food culture seems to be in a transitional state in which both healthy eating as well as sustainable consumption strategies are contributing to shaping the future school food culture. It is therefore imperative to study how these changes in agendas influences each other and to study the associations between healthy eating and organic supply strategies at school. This has been the point of departure for Working Package 5 (WP5): Nutrition and Health. The WP5 study has included Denmark, Norway, Germany, Finland and Italy. The WP has been asking questions about the possible spin offs and ramification on nutrition and health that the emerging public organic food strategies might have had. The WP is a part of the project “innovative Public Organic food Procurement for Youth” (iPOPY) and the WP5 has been carried out by Aalborg University Denmark. The research presented here has been conducted in Germany, Finland, and Italy

The effect of sheared diamagnetic flow on turbulent structures generated by the Charney–Hasegawa–Mima equation

The generation of electrostatic drift wave turbulence is modelled by the Charney–Hasegawa–Mima equation. The equilibrium density gradient n0=n0(x) is chosen so that dn0 /dx is nonzero and spatially variable (i.e., v*e is sheared). It is shown that this sheared diamagnetic flow leads to localized turbulence which is concentrated at max(grad n0), with a large dv*e/dx inhibiting the spread of the turbulence in the x direction. Coherent structures form which propagate with the local v*e in the y direction. Movement in the x direction is accompanied by a change in their amplitudes. When the numerical code is initialized with a single wave, the plasma behaviour is dominated by the initial mode and its harmonics

RAINIER: A Simulation Tool for Distributions of Excited Nuclear States and Cascade Fluctuations

A new code has been developed named RAINIER that simulates the $\gamma$-ray decay of discrete and quasi-continuum nuclear levels for a user-specified range of energy, angular momentum, and parity including a realistic treatment of level spacing and transition width fluctuations. A similar program, DICEBOX, uses the Monte Carlo method to simulate level and width fluctuations but is restricted to $\gamma$-ray decay from no more than two initial states such as de-excitation following thermal neutron capture. On the other hand, modern reaction codes such as TALYS and EMPIRE populate a wide range of states in the residual nucleus prior to $\gamma$-ray decay, but do not go beyond the use of deterministic functions and therefore neglect cascade fluctuations. This combination of capabilities allows RAINIER to be used to determine quasi-continuum properties through comparison with experimental data. Several examples are given that demonstrate how cascade fluctuations influence experimental high-resolution $\gamma$-ray spectra from reactions that populate a wide range of initial states.Comment: 14 pages, 13 figures, Nuclear Instrumentation and Methods A, 201