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Open Access Publications from the University of California

Scholarly Works (5 results)

  • Article
  • Peer Reviewed
Berkeley Research Impact Initiative (BRII) (2014)
A web-based, general-purpose simulation and modeling tool is presented in this paper. The tool, Insight Maker, has been designed to make modeling and simulation accessible to a wider audience of users. Insight Maker integrates three general modeling approaches – System Dynamics, Agent-Based Modeling, and imperative programming – in a unified modeling framework. The environment provides a graphical model construction interface that is implemented purely in client-side code that runs on users’ machines. Advanced features, such as model scripting and an optimization tool, are also described. Insight Maker, under development for several years, has gained significant adoption with currently more than 20,000 registered users. In addition to detailing the tool and its guiding philosophy, this first paper on Insight Maker describes lessons learned from the development of a complex web-based simulation and modeling tool.
    • Thesis
    • Peer Reviewed
    UC Berkeley Electronic Theses and Dissertations (2014)

    Predictive accuracy of a model is of key importance in research and to a lay audience. Diverse modeling methods and parameter estimation methods exist, such that a wide range of techniques are available from which to select when approaching a modeling task. Given this, two questions naturally arise in relation to a modeling task: model selection and model parameter estimation. This dissertation is intended to advance the theory and practice of model selection and parameter estimation for the topics discussed here.

    * In Chapter 2, I develop A3, a novel method for assessing predictive accuracy and enabling direct comparisons between competing models in an accessible framework. This method uses resampling techniques to "wrap" predictive modeling methods and estimate a standard set of error metrics for both the model as a whole and additionally for each explanatory variable utilized by the model. Two case studies in the chapter illustrate the applied utility of the method and how improved models may not only result in increased predictive accuracy, but also potentially alter inferences and conclusions about the effects of parameters in the model. An R package implementing the method is made available on CRAN.

    * In Chapter 3, I develop ICE, a novel method of home range estimation. ICE uses a competitive method for estimating home ranges. Effectively, an estimator of estimators, ICE pits existing home range estimators against each other, each of which may be best suited for a given type of data. By selecting between different approaches, ICE can theoretically improve on the performance of any individual estimator across heterogeneous data sets.

    * In Chapter 4, I develop Contingent Kernel Density Estimation, an extension to Kernel Density Estimation designed to account for the case when observations are measured with a specific form of error. Chapter 4 develops the method and derives contingent kernels for commonly-used kernels and sampling regimes. An application of the method is presented to data collected from the social networking site, Twitter, to estimate the national distribution of a sample of Twitter users.

    * The study in Chapter 5 analyzes a large data set collected from Twitter. This study is based on data from over four million Twitter users and estimates parameters of this population with a primary focus on color preference choices made by these users. Novel results are found in this "big data" analysis approach that may not have been able to be identified with earlier, traditional approaches of sampling and surveying the behavior of individuals.

      Cover page: Methods for Comparative Model Selection and Parameter Estimation in Diverse Modeling Applications
      • Article
      • Peer Reviewed
      Berkeley Research Impact Initiative (BRII) (2012)
      Kernel density estimation is a widely used method for estimating a distribution based on a sample of points drawn from that distribution. Generally, in practice some form of error contaminates the sample of observed points. Such error can be the result of imprecise measurements or observation bias. Often this error is negligible and may be disregarded in analysis. In cases where the error is non-negligible, estimation methods should be adjusted to reduce resulting bias. Several modifications of kernel density estimation have been developed to address specific forms of errors. One form of error that has not yet been addressed is the case where observations are nominally placed at the centers of areas from which the points are assumed to have been drawn, where these areas are of varying sizes. In this scenario, the bias arises because the size of the error can vary among points and some subset of points can be known to have smaller error than another subset or the form of the error may change among points. This paper proposes a “contingent kernel density estimation” technique to address this form of error. This new technique adjusts the standard kernel on a point-by-point basis in an adaptive response to changing structure and magnitude of error. In this paper, equations for our contingent kernel technique are derived, the technique is validated using numerical simulations, and an example using the geographic locations of social networking users is worked to demonstrate the utility of the method.
        • Article
        • Peer Reviewed
        San Francisco Estuary and Watershed Science, Volume 10, Issue 4 (2012)

        Adult salmon that stray when they escape into non-natal streams to spawn is a natural phenomenon that promotes population growth and genetic diversity, but excessive stray rates impede adult abundance restoration efforts. Adult San Joaquin River (SJR) Basin fall-run Chinook salmon (Oncorhynchus tshawytscha) that return to freshwater to spawn migrate through the San Francisco Bay and Sacramento–San Joaquin River Delta (Delta). The Delta has been heavily affected by land development and water diversion. During the fall time-period for the years 1979 to 2007 Delta pumping facilities diverted on average 340% of the total inflow volume that entered the Delta from the SJR. The hypothesis tested in this paper is that river flow and Delta exports are not significantly correlated with SJR salmon stray rates. Adult coded-wire-tagged salmon recoveries from Central Valley rivers were used to estimate the percentage of SJR Basin salmon that strayed to the Sacramento River Basin. SJR salmon stray rates were negatively correlated (P = 0.05) with the average magnitude of pulse flows (e.g., 10 d) in mid- to late-October and positively correlated (P = 0.10) with mean Delta export rates. It was not possible to differentiate between the effects of pulse flows in October and mean flows in October and November on stray rates because of the co-linearity between these two variables. Whether SJR-reduced pulse flow or elevated exports causes increased stray rates is unclear. Statistically speaking the results indicate that flow is the primary factor. However empirical data indicates that little if any pulse flow leaves the Delta when south Delta exports are elevated, so exports in combination with pulse flows may explain the elevated stray rates. For management purposes, we developed two statistical models that predict SJR salmon stray rate: (1) flow and export as co-independent variables; and (2) south Delta Export (E) and SJR inflow (I) in the form of an E:I ratio.

         

        • 1 supplemental PDF
        Cover page: Delta Flow Factors Influencing Stray Rate of Escaping Adult San Joaquin River Fall-Run Chinook Salmon (<em>Oncorhynchus tshawytscha</em>)Creative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2007)
        Parametric kernel methods currently dominate the literature regarding the construction of animal home ranges (HRs) and utilization distributions (UDs). These methods frequently fail to capture the kinds of hard boundaries common to many natural systems. Recently a local convex hull (LoCoH) nonparametric kernel method, which generalizes the minimum convex polygon (MCP) method, was shown to be more appropriate than parametric kernel methods for constructing HRs and UDs, because of its ability to identify hard boundaries (e.g., rivers, cliff edges) and convergence to the true distribution as sample size increases. Here we extend the LoCoH in two ways: "fixed sphere-of-influence," or r-LoCoH (kernels constructed from all points within a fixed radius r of each reference point), and an "adaptive sphere-of-influence," or a-LoCoH (kernels constructed from all points within a radius a such that the distances of all points within the radius to the reference point sum to a value less than or equal to a), and compare them to the original "fixed-number-of-points," or k-LoCoH (all kernels constructed from k-1 nearest neighbors of root points). We also compare these nonparametric LoCoH to parametric kernel methods using manufactured data and data collected from GPS collars on African buffalo in the Kruger National Park, South Africa. Our results demonstrate that LoCoH methods are superior to parametric kernel methods in estimating areas used by animals, excluding unused areas (holes) and, generally, in constructing UDs and HRs arising from the movement of animals influenced by hard boundaries and irregular structures (e.g., rocky outcrops). We also demonstrate that a-LoCoH is generally superior to k- and r-LoCoH (with software for all three methods available at http://locoh.cnr.berkeley.edu).
          Cover page: LoCoH: Nonparameteric Kernel Methods for Constructing Home Ranges and Utilization Distributions
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