A Tour of Trellis Graphics

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ABSTRACT This document leads you through Trellis graphics: it shows the functions in the Trellis library, it describes the common arguments that the functions share, and shows how Trellis displays are customized for various graphical devices. Other information is available about Trellis, including a user's manual and a journal article with data analysis examples. To find these and more, refer to the Trellis web page:

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    ABSTRACT: The most common techniques for graphically presenting a multivariate dataset involve projection onto a one or two-dimensional subspace. Interpretation of such plots is not always straightforward because projections are smoothing operations in that structure can be obscured by projection but never enhanced. In this paper an alternative procedure for finding interesting features is proposed that is based on locating the modes of an induced hyperspherical density function, and a simple algorithm for this purpose is developed. Emphasis is placed on identifying the non-linear effects, such as clustering, so to this end the data are firstly sphered to remove all of the location, scale and correlational structure. A set of simulated bivariate data and artistic qualities of painters data are used as examples.
    Statistics and Computing 11/1998; 8(4):347-355. · 1.75 Impact Factor
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    ABSTRACT: The Phenotype MicroArray (OmniLog® PM) system is able to simultaneously capture a large number of phenotypes by recording an organism's respiration over time on distinct substrates. This technique targets the object of natural selection itself, the phenotype, whereas previously addressed '-omics' techniques merely study components that finally contribute to it. The recording of respiration over time, however, adds a longitudinal dimension to the data. To optimally exploit this information, it must be extracted from the shapes of the recorded curves and displayed in analogy to conventional growth curves. The free software environment R was explored for both visualizing and fitting of PM respiration curves. Approaches using either a model fit (and commonly applied growth models) or a smoothing spline were evaluated. Their reliability in inferring curve parameters and confidence intervals was compared to the native OmniLog® PM analysis software. We consider the post-processing of the estimated parameters, the optimal classification of curve shapes and the detection of significant differences between them, as well as practically relevant questions such as detecting the impact of cultivation times and the minimum required number of experimental repeats. We provide a comprehensive framework for data visualization and parameter estimation according to user choices. A flexible graphical representation strategy for displaying the results is proposed, including 95% confidence intervals for the estimated parameters. The spline approach is less prone to irregular curve shapes than fitting any of the considered models or using the native PM software for calculating both point estimates and confidence intervals. These can serve as a starting point for the automated post-processing of PM data, providing much more information than the strict dichotomization into positive and negative reactions. Our results form the basis for a freely available R package for the analysis of PM data.
    PLoS ONE 04/2012; 7(4):e34846. · 3.53 Impact Factor


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