The gridGraphviz package renders node-and-edge graphs in R using the grid graphics package. Graphs are laid out using the Rgraphviz package to interface with the graph layout algorithms in graphviz. This article details the improvements made between gridGraphviz versions 0.2 and 0.3, including: support for “ellipse”- and “polygon”-shaped nodes; handling of edges in undirected graphs; support for various new arrow types; and support for edge labels. Version 0.3 also introduces a method to produce graphs with an overall size closer to graphviz’s output.
Ashley Noel Hinton and Paul Murrell
The grImport2 package imports vector images that are stored in the SVG image format for inclusion within images generated by R. The original grImport package performs the same task, but instead using PostScript images as its source image format. This technical report describes the steps taken to improve not only the grImport package, but also follows the development of two new packages, grImport2 and grConvert. The latter, grConvert, converts images from popular vector image formats (PostScript, PDF and SVG) into valid input formats for grImport and grImport2. The grImport2 package is an entirely new package that does not suffer from some limitations of the grImport package, whose limitations are primarily due to the dependence on the PostScript image format.
Simon Potter and Paul Murrell
This Literature Review provides an Overview of Open Data in New Zealand by first defi ning Open Data, including key desirable properties and terminology relevant to the discussion, followed by an Overview of New Zealand State Sector sources. The State Sector organisations covered are those listed as Public Service departments on the State Services Commission’s website (http://www.ssc.govt.nz/state_sector_organisations).
This article discusses the importance of providing structure and labelling within SVG code, particularly when the SVG code is generated indirectly by a high-level system and when the SVG code describes a complex image such as a statistical plot. We argue that this is a desirable goal, but that many high-level systems that generate SVG do not provide sufficient structure and labelling. An example of a system, based on R, that does provide structure and labelling, is described to demonstrate that the goal is acheivable and we highlight the crucial features of this system that we see as important factors in achieving this goal.
Paul Murrell and Simon Potter.
The gridSVG package exports grid images to the SVG image format for viewing on the web. This article describes the problems associated with retaining grid object names in SVG element id attributes. In addition, new features in gridSVG that allow manipulation and retrieval of generated id attributes are discussed. These new features allow for easier and more predictable development of interactivity in plots generated by gridSVG.
Simon Potter and Paul Murrell
Competitive exclusion embodies the idea of the first mover advantage where species or populations arriving first at a suitable location prevent secondary colonisation of the already occupied site.
While adaptation to environmental variables (e.g., temperature, altitude, etc.) is essential, the presence or absence of certain species at a particular location often depends on whether or not competing species co-occur. In particular, competition could explain observed patterns of low genetic and phenotypic diversity following rapid colonisation events in Europe as well as the “progression” pattern in the phylogenies of species found on various islands along the Hawaiian archipelago. Competitive exclusion has been absent from past quantitative analyses because of the difficulty in designing adequate methods for assessing its impact. We present here a new statistical framework that integrates competition along with limited dispersal into a Bayesian phylogenetic model of migration. Using simulations, we assess the performance of our approach and demonstrate its ability to detect competition from the comparative analysis of homologous genetic sequences using geographic information.
Statistical plots drawn with the ggplot2 package generate numerous grid grobs and viewports which are labelled and organised into a coherent hierarchy. This report describes an example that shows how to manipulate the grobs and viewports in a ggplot2 plot using tools from the grid package, export the result to SVG using gridSVG, then manipulate the result further using XML tools, to produce an interactive ggplot2 graphic for the web.
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
The selectr package translates a CSS selector into an equivalent XPath expression. This allows the use of CSS selectors to query XML documents using the XML package. Convenience functions are also provided to mimic functionality present in modern web browsers.