2014-01 Improving the ‘gridGraphviz’ package in R

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


2013-9 Improved Importing of Vector Graphics in R

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

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2013-5 Open Data in New Zealand

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).

Jimmy Oh.


2013-4 Generating Structured and Labelled SVG

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.


2013-3 Generating unique names in gridSVG

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


2013-2 Modelling competitive exclusion and limited dispersal in a statistical phylogeographic framework

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.

Stephane Guindon


2013-1 TimingManager: Animation Sequences in JavaScript

The TimingManager library is a tool written in JavaScript used to apply animations in a web browser. It is not concerned with creation or modification of animation timing information, and delegates those tasks to R via the animaker package. Primarily TimingManager is focused on assigning actions to existing animations, then playing animation sequences using either a declarative or frame-based approach.

Simon Potter


2012-12 Post-Processing grid Graphics

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.

Paul Murrell


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