2012-11 Generating Animation Sequence Descriptions

This report describes the animaker package for generating descriptions of animation sequences. An animation sequence is composed by combining atomic animations in series to create sequence animations or in parallel to create track animations. Functions are provided for manipulating animation sequences, generating timing schemes from animation sequences, and producing diagrams to visualise animation sequences.

Paul Murrell and Simon Potter

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2012-9 Writing grid Extensions

New hook functions, makeContext() and makeContent(), have been added to the grid graphics package. These functions allow an alternative approach to developing custom grobs when a grob can only decide what to draw at drawing time rather than when the grob is created. For custom grobs that are based on this new approach, the

grid.force() function provides access to low-level grobs that are otherwise invisible because they are only generated at drawing time.

These functions lead to greater flexibility in the development of custom grobs and more power to modify the result after drawing is complete.

Paul Murrell

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2012-8 Meta-analysis of a rare-variant association test

Genome-wide assocation studies have often been carried out by meta-analysis rather than by pooling individual-level data.  For one-dimensional parameter estimates and the corresponding tests of association these meta-analyses lead to essentially no loss of information relative to pooling individual data.  The situation is different for multi-parameter tests, such as the omnidirectional rare-variant tests being used in resequencing studies.  In this paper we consider one popular rare-variant test, a version of the sequence kernel association test.  We show that meta-analyses based on the $p$-value or test statistic from each contributing study are importantly less efficient than an analysis pooling individual data, but that a more sophisticated meta-analysis retains full efficiency. The meta-analysis is based on a reformulation of the test that links it to tests used in survey analysis.

Thomas Lumley, Jennifer Brody, Josee Dupuis, Adrienne Cupples

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2012-7 A Structured Approach for Generating SVG

The gridSVG package exports grid images to an SVG format for viewing on the web. This article describes a new development in the way that gridSVG produces the SVG output. The result is greater flexibility in how the SVG output is produced and increased opportunities to manipulate the SVG output, which creates new possibilities for generating more complex and sophisticated dynamic and interactive R graphics for the web.

Simon Potter and Paul Murrell

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2012-6 Working with the gridSVG Coordinate System

The gridSVG package exports grid images to an SVG format for viewing on the web. This article describes new features in gridSVG that allow grid coordinate system information to be exported along with the image. This allows the SVG image to be modified dynamically in a web browser, with full knowledge of coordinate system information, such as the scales on plot axes. As a consequence, it is now possible to create more complex and sophisticated dynamic and interactive R graphics for the web.

Simon Potter and Paul Murrell

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2012-5 Voronoi Treemaps in R

A Voronoi Treemap is a visualisation tool for displaying data with a hierarchical structure.  This article describes an open source implementation of Voronoi Treemaps in the R language and environment for statistical computing and graphics.  The article includes example usage for the main R functions and a detailed description of the underlying code.  The raw code itself is also available with this article.

Paul Murrell

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2012-4 Two-sample rank tests under complex sampling

Rank tests are widely used for exploratory and formal inference in the health and social sciences.  With the increasing use of data from complex survey samples in medical research, there is increasing demand for versions of rank tests that account for the sampling design. In the absence of design-based rank tests, naive unweighted rank tests are being used in survey analyses even by researchers who otherwise use inferential methods appropriate for the sampling design. We propose a general approach to constructing design-based rank tests when comparing groups within a complex sample and when using a national survey as a reference distribution, and illustrate both scenarios with examples.  We show that the tests have asymptotically correct level and that the relative power of different rank tests is not greatly affected by complex sampling.

Thomas Lumley, Alastair Scott

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2012-3 An empirical-process central limit theorem for complex sampling under bounds on the design effect

Uniform central limit theorems (`Donsker theorems’) have been widely useful in semiparametric statistics, both under iid sampling and for stationary sequences and random fields. Only limited results have been available under complex sampling, especially multistage sampling. In this note we derive a complex-sampling analogue of Ossiander’s bracketing-entropy conditions for a uniform central limit theorem, under the assumption that certain design effects are uniformly bounded. We discuss the plausibility of this assumption in realistic surveys.

Thomas Lumley

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2012-2: Two-phase subsampling designs for genomic resequencing studies

Targeted resequencing of DNA at specific genes or other genomic loci is now feasible for hundreds or thousands of samples, and costs for larger-scale resequencing are decreasing rapidly. For at least the next few years, resequencing will need to be confined to small subsets of the large samples on which genome-wide association studies have been recently been performed. This paper describes some strategies for subsampling an existing cohort for resequencing, and flexibly analysing the resulting data. We illustrate these strategies by describing the actual design and planned analyses for the example that motivated our research, the CHARGE-S resequencing study carried out by the CHARGE (Cohorts in Heart and Aging Research in Genomic Epidemiology) Consortium.

Thomas Lumley, Josee Dupuis, Kenneth M. Rice, Maja Barbalic, Joshua C. Bis, L. Adrienne Cupples, Bruce M. Psaty, Christopher J. O’Donnell, Eric Boerwinkle

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