Probabilistic Programming in Python using PyMC

Probabilistic programming (PP) allows flexible specification of Bayesian statistical models in code. PyMC3 is a new, open-source PP framework with an intutive and readable, yet powerful, syntax that is close to the natural syntax statisticians use to describe models. It features next-generation Markov chain Monte Carlo (MCMC) sampling algorithms such as the No-U-Turn Sampler (NUTS; Hoffman, 2014), a self-tuning variant of Hamiltonian Monte Carlo (HMC; Duane, 1987). Probabilistic programming in Python confers a number of advantages including multi-platform compatibility, an expressive yet clean and readable syntax, easy integration with other scientific libraries, and extensibility via C, C++, Fortran or Cython. These features make it relatively straightforward to write and use custom statistical distributions, samplers and transformation functions, as required by Bayesian analysis

A System Dynamics Approach for Information Technology Implementation and Sustainment

The goal of this research is to bring a new, dynamic modeling perspective to organizational information technology (IT) implementation systems (using the Air Force GeoBase initiative as a real-world example) without compromising principles from the research literature. Undesired behavior patterns, from historically poor IT implementation performance, versus desired behavior patterns are incorporated into the model structure. Using a system dynamics approach, multiple simulation runs under various initial conditions and organizational contexts are performed and compared over a short-term versus a long-term period of time. Based on these simulation ruins, various mixes of management interventions, under varying conditions, are recommended to improve IT implementation performance based on manager and organizational goals

Municipal Lighting of Logan City

Municipal lighting in Logan City is a contemporary development of municipal lighting in other American cities, because it has involved public opinion and lawsuits and competition between a private corporation and a municipality owning and operating an electric light plant. It is perhaps one of the most eventful and serious conflicts between owners of a public utility which has some before public and legal observation in the State of Utah. The case of Logan City vs. Utah Power & Light Company was brought before the Utah State Utilities Commission and the Utah State Supreme Court and the Court decided that the Utilities Commission did not have the jurisdiction to regulate the rates and the policies of municipally owned utilities. This case will have a bearing on future conflicts between municipally owned and privately owned public utilities operating within the State of Utah

Release of Large Water Droplets

Water is familiar to all human beings and water droplets are an integral part of our daily lives. From irrigation sprinklers to waterfalls we can observe the formation of water droplets. For most, the droplets are so common and mundane that no thought is given to how the droplets form. Scientists have spent many decades detailing the processes that lead to droplet formation. Current theories and experiments agree quite well for specific cases such as pendant drop formation and jet breakup, but in regards to large volumes of free falling liquid there is very little experimental work to confirm the theory. This is due to the difficulty of suspending large volumes of liquid in a repeatable way. This paper details a new method for suspending large volumes of liquid in a repeatable and predictable way. The paper also describes the initial shapes and behavior the liquid volumes may inherit from the release method. The new method uses a simple pendulum and hydrophobic surfaces to suspend large droplets. The hydrophobic surfaces vary from flat solid surfaces to spherical mesh surfaces. High speed cameras record the droplets which provides the shape and behavior data. The shapes of the droplets are described as ”modes”. More than one mode can exist in the droplet at a given time. The amplitude of a mode describes the size of the mode. The larger the amplitude the more a mode dominates the overall shape of the droplet. Ideally, the droplet mechanism in this paper would create spherical droplets or droplets with zero-amplitude modes. A mesh hydrophobic surface produces the most spherical droplets (i.e., smallest amplitude) for large volumes. The droplets in this paper range from diameters of 4.0-15.8 mm (0.034-2.08 mL)

Aplicación de la modelación integrada bayesiana y de los métodos Monte Carlo basados en cadenas de Markov para la conservación de una especie recolectada

When endeavoring to make informed decisions, conservation biologists must frequently contend with disparate sources of data and competing hypotheses about the likely impacts of proposed decisions on the resource status. Frequently, statistical analyses, modeling (e.g., for population projection) and optimization or simulation are conducted as separate exercises. For example, a population model might be constructed, whose parameters are then estimated from data (e.g., ringing studies, population surveys). This model might then be used to predict future population states, from current population estimates, under a particular management regime. Finally, the parameterized model might also be used to evaluate alternative candidate management decisions, via simulation, optimization, or both. This approach, while effective, does not take full advantage of the integration of data and model components for prediction and updating; we propose a hierarchical Bayesian context for this integration. In the case of American black ducks (Anas rubripes), managers are simultaneously faced with trying to extract a sustainable harvest from the species, while maintaining individual stocks above acceptable thresholds. The problem is complicated by spatial heterogeneity in the growth rates and carrying capacity of black ducks stocks, movement between stocks, regional differences in the intensity of harvest pressure, and heterogeneity in the degree of competition from a close congener, mallards (Anas platyrynchos) among stocks. We have constructed a population life cycle model that takes these components into account and simultaneously performs parameter estimation and population prediction in a Bayesian framework. Ringing data are used to develop posterior predictive distributions for harvest mortality rates, given as input decisions about harvest regulations. Population surveys of black ducks and mallards are used to obtain stock–specific estimates of population size for both species, for inputs into the population life–cycle model. These estimates are combined with the posterior distributions for harvest mortality, to obtain posterior predictive distributions of future population status for candidate sets of regional harvest regulations, under alternative biological hypotheses for black duck population dynamics. These distributions might then be used for both the exploration of optimal harvest policies and for sequential updating of model posteriors, via comparison of predictive distributions to future survey estimates of stock–specific abundance. Our approach illustrates advantages of MCMC for integrating disparate data sources into a common predictive framework, for use in conservation decision making.En el momento de tomar decisiones bien fundamentadas, es habitual que los biólogos conservacionistas deban enfrentarse a fuentes de datos dispares e hipótesis alternativas acerca de los impactos probables que tendrán las decisiones propuestas en el estado del recurso. A menudo, tanto los análisis estadísticos, como la modelación (para la proyección poblacional, por ejemplo) y la optimización o simulación, se llevan a cabo como ejercicios independientes. Así, es posible que se construya un modelo poblacional, cuyos parámetros se estimen a partir de datos (como estudios de anillamiento y estudios poblacionales). Posteriormente, cabe la posibilidad de que este mismo modelo se emplee para predecir situaciones demográficas futuras a partir de las estimaciones de población actuales, utilizando para ello un sistema de gestión determinado. Por último, el modelo parametrizado también puede emplearse para evaluar posibles decisiones de gestión alternativas, a través de la simulación, la optimización, o ambos procedimientos. Si bien este enfoque resulta eficaz, no aprovecha al máximo la integración de datos y los componentes de los modelos para la predicción y actualización. En este estudio proponemos un contexto bayesiano jerárquico que permite efectuar dicha integración. En el caso del ánade sombrío americano (Anas rubripes), los gestores deben enfrentarse a la labor de intentar extraer una recolección sostenible de la especie, al tiempo que mantienen los stocks de individuos por encima de umbrales aceptables. El problema se ve agravado por la heterogeneidad espacial que presentan las tasas de crecimiento y la carga cinegética de los stocks de ánades sombríos, el movimiento entre los stocks, las diferencias regionales en la intensidad de la presión recolectora y la heterogeneidad en el grado de competencia por parte de un congénere cercano —el ánade real (Anas platyrynchos)— entre los stocks. Hemos formulado un modelo del ciclo vital de la población que toma en consideración estos componentes, al tiempo que permite llevar a cabo una estimación de los parámetros y una predicción de la población en un marco bayesiano. Los datos de anillamiento se emplean para desarrollar distribuciones predictivas posteriores para las tasas de mortalidad durante la recolección, expresadas como decisiones de entrada acerca de la normativa sobre recolecciones. Los estudios poblacionales del ánade sombrío y del ánade real se emplean para obtener estimaciones sobre el tamaño poblacional específicas de los stocks de ambas especies, que se emplearán como entradas para el modelo del ciclo vital de la población. Dichas estimaciones se combinan con las distribuciones posteriores para la mortalidad durante la recolección, con el propósito de obtener distribuciones predictivas posteriores de la situación demográfica futura para posibles conjuntos de normativas regionales acerca de la recolección, de acuerdo con hipótesis biológicas alternativas relativas a la dinámica poblacional del ánade sombrío. En una fase posterior, tales distribuciones pueden utilizarse tanto para la investigación de políticas óptimas en materia de recolección, como para la actualización secuencial de distribuciones posteriores del modelo mediante la comparación de distribuciones predictivas para estimaciones en estudios futuros acerca de la abundancia poblacional presente de forma específica en los stocks. Nuestro enfoque ilustra las ventajas que presentan las técnicas de Montecarlo basadas encadenas de Markov (MCMC) para integrar fuentes de datos dispares en un marco predictivo común, con vistas a su utilización en la toma de decisiones sobre conservación

On the Threshold of Drop Fragmentation under Impulsive Acceleration

We examine the complete landscape of parameters which affect secondary breakup of a Newtonian droplet under impulsive acceleration. A Buckingham-Pi analysis reveals that the critical Weber number $\mathit{We}_\mathit{cr}$ for a non-vibrational breakup depends on the density ratio $(\rho)$, the drop $(\mathit{Oh}_d)$ and the ambient $(\mathit{Oh}_o)$ Ohnesorge numbers. Volume of fluid (VOF) multiphase flow simulations are performed using Basilisk to conduct a reasonably complete parametric sweep of the non-dimensional parameters involved. It is found that, contrary to current consensus, even for $\mathit{Oh}_d \leq 0.1$, a decrease in $\mathit{Oh}_d$ has a substantial impact on the breakup morphology, motivating plume formation. In addition to $\rho$, $\mathit{Oh}_o$ also affects the balance between pressure differences between a droplet's pole and its periphery, and the shear stresses on its upstream surface, which ultimately dictates the flow inside the droplet. This behavior manifests in simulations through the observed pancake shapes and ultimately the breakup morphology (forward or backward bag). All these factors affecting droplet deformation process are specified and theories explaining the observed results are provided. A $\mathit{We}_\mathit{cr}-\mathit{Oh}_d$ plot is provided to summarize all variations in $\mathit{We}_\mathit{cr}$ observed due to changes in the involved non-dimensional parameters. All observed critical pancake and breakup morphologies are summarized using a phase diagram illustrating all deformation paths a droplet might take under impulsive acceleration. Finally, based on the understanding of process of bag breakup gained from this work, a non-dimensional parameter to predict droplet breakup threshold is derived and tested on all simulation data obtained from this work and all experimental data gathered from existing literature

Quantitative analysis of hydrogen gas formed by aqueous corrosion of metallic uranium

Three unirradiated EBR-II blanket fuel samples containing depleted uranium metal were corrosion tested in simulated J-13 well water at 90 C. The corrosion rate of the blanket uranium metal was then determined relative to H{sub 2} formation. Corrosion of one of the samples was interrupted prior to complete oxidation of the uranium metal and the solid corrosion product was analyzed for UO{sub 2} and UH{sub 3}

An Adaptive Decision Framework for the Conservation of a Threatened Plant

This is the publisher's version, also available electronically from http://www.fwspubs.org/.Mead's milkweed Asclepias meadii, a long-lived perennial herb of tallgrass prairie and glade communities of the central United States, is a species designated as threatened under the U.S. Endangered Species Act. Challenges to its successful management include the facts that much about its life history is unknown, its age at reproductive maturity is very advanced, certain life stages are practically unobservable, its productivity is responsive to unpredictable environmental events, and most of the known populations occur on private lands unprotected by any legal conservation instrument. One critical source of biological uncertainty is the degree to which fire promotes growth and reproductive response in the plant. To aid in its management, we developed a prototype population-level state-dependent decision-making framework that explicitly accounts for this uncertainty and for uncertainties related to stochastic environmental effects and vital rates. To parameterize the decision model, we used estimates found in the literature, and we analyzed data from a long-term monitoring program where fates of individual plants were observed through time. We demonstrate that different optimal courses of action are followed according to how one believes that fire influences reproductive response, and we show that the action taken for certain population states is informative for resolving uncertainty about competing beliefs regarding the effect of fire. We advocate the use of a model-predictive approach for the management of rare populations, particularly when management uncertainty is profound. Over time, an adaptive management approach should reduce uncertainty and improve management performance as predictions of management outcome generated under competing models are continually informed and updated by monitoring data

Joint estimation of crown of thorns (Acanthaster planci) densities on the Great Barrier Reef

Crown-of-thorns starfish (CoTS; Acanthaster spp.) are an outbreaking pest among many Indo-Pacific coral reefs that cause substantial ecological and economic damage. Despite ongoing CoTS research, there remain critical gaps in observing CoTS populations and accurately estimating their numbers, greatly limiting understanding of the causes and sources of CoTS outbreaks. Here we address two of these gaps by (1) estimating the detectability of adult CoTS on typical underwater visual count (UVC) surveys using covariates and (2) inter-calibrating multiple data sources to estimate CoTS densities within the Cairns sector of the Great Barrier Reef (GBR). We find that, on average, CoTS detectability is high at 0.82 [0.77, 0.87] (median highest posterior density (HPD) and [95% uncertainty intervals]), with CoTS disc width having the greatest influence on detection. Integrating this information with coincident surveys from alternative sampling programs, we estimate CoTS densities in the Cairns sector of the GBR averaged 44 [41, 48] adults per hectare in 2014