Friday, 29 June 2012

PhD week 17: A tutorial on shading curves in Inkscape

As part of my research, I will need to illustrate anatomical structures that are useful for the identification of the weevils that I will be working with. I intend to use a combination of photographs and line drawings, using the different formats in different situations. Photos will be used in some instances (i.e. habitus images) to give a realistic idea of what the creatures look like. In some cases though, photographs give too much information, and line drawings are the way to go. To create my line drawings, I will be using the free and open-source vector graphics program Inkscape.

As the structures I will be working with are 3-dimensional, I want to convey that (to a degree) in my illustrations. Traditional line drawings would depict this by using the method of stippling. If this is replicated in Inkscape, the resulting file becomes massive and unwieldly, due to the huge number of dots that it has to handle. The digital way of doing this it to use gradients. Unfortunately, curved gradients are not supported in the SVG specifications, which means we have to fake it. A method for doing this is presented below.

Wednesday, 27 June 2012

PhD week 16: Wellington

New Zealand Tango Festival 2012
The teachers dance at the New Zealand Tango Festival 2012

I spent most of the past week in Wellington, spending a day in the Te Papa insect collection, three days dancing Tango as part of the New Zealand Tango Festival, and the rest of the time wandering around the city and the botanic gardens. All events were extremely pleasant and we arrived back in Christchurch sore and tired from doing too much dancing until too early in the mornings, but extremely pleased that we went.

One of the most exciting things of my time there was the unexpected discovery of the syntypes of a species described by Thomas Broun. These were the first type specimens that I have seen, and it was great finding them, recognising what they were, and being able to put a name to some previously unidentified specimens in my collection. It was also a rather amazing experience to look at specimens that Broun himself had looked at and handled nearly 100 years ago.

Psalms 68–70,

Biodiversity Heritage Library Photostream
Curiosities of biological nomenclature

Planet Dinosaur
Star Trek: Deep Space Nine Season 4

Sunday, 17 June 2012

PhD week 15: Proposal

This week I gave my proposal seminar to the department. This is an opportunity for starting postgraduate students to present their research intentions to their colleagues. They are a formal part of the process of starting into postgraduate research, but they tend not to be too scary. In my case I was able to enjoy a talk time of around 25 minutes, followed by a 15 minute discussion about various details of my research. It was a good experience, but one that I'm pleased to have behind me as now I can concentrate on other, more fun things (like looking at weevils!).

My presentation (the title slide is shown above) was formatted with the beamer package for LaTeX, using a customised style that incorporates the navigation bar on top of a coloured sidebar. This theme emulates the Bio-Protection Research Centre's presentation template, while allowing it to be created with LaTeX. A zip file containing the style files is available on gitHub.

In other news, I started using git as the version control tool for my thesis writing activities. I will be using this in conjunction with Dropbox to achieve the multiple aims of: 1) keeping track of the changes I make to my thesis and associated files, allowing me to go back to previous versions if necessary, 2) having a backup of my work "in the cloud", and 3) being able to access my thesis writing from multiple computers. I was assisted in this task by the documentation for git that guides one through making a repository from an existing folder, and StackOverflow questions regarding using git for writing a thesis and using git with dropbox.

   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 63–64,

New Zealand Plant Radiation Network
Wikipedia—Liturgy of the hours
Hadley Wickham's R style guide
LibriVox—acoustical liberation of books in the public domain
XeTeX and LaTeX blog—Newcommand with an optional argument—out-of-copyright audiobooks

Facedown Records Summer Sampler 2012
Kyrie eleison
Gotan Project—Tango 3.0

Eagle Eye

Monday, 11 June 2012

An R function for finding coordinates of NZ localities

Over the course of my PhD, I will be doing a fair amount of georeferencing. This involves obtaining geographic coordinates for localities where weevil specimens have been collected. When I'm the one who has collected them, this is fairly straightforward—Google Maps has made obtaining coordinates a breeze. When it's a museum specimen, however, things get a little tricky. Maps and atlases are extremely useful, but hard to search through. The university has access to MapToaster which contains the topographic maps of New Zealand, and which allows one to search for place names. However, it's only available from university computers, and the search feature requires a degree of mouse work to drive it. LINZ has made the New Zealand Geographic Place Names Database freely available online, which is also fairly fiddly to use in a high throughput situation. However, it is based on a fairly well-structured database, which allowed me to write an R function to search and retrieve information (including coordinates) for place names of interest.

The result is gazNZ(). This function allows a name to be searched for from the R console, making the process of finding coordinates a lot quicker, and means that I only need to use my keyboard when searching for things—a much more satisfying state of affairs.

> gazNZ("Cook Strait")
Read 201 items
Read 211 items
$`Cook Strait`
[1] -41.2493 174.4736

Saturday, 9 June 2012

PhD week 14: Snow

This week has been disrupted a few times. Monday was Queen's Birthday public holiday, then on Wednesday we woke up to the scene above—beautiful, but cold and not conducive to getting into the university. As we're not especially partial to the cold, we spent the day inside keeping warm, and reading and doing homely jobs that needed to be done. I also utilised the day productively by learning more about the XML package for R, and how to access XML data using Xpath. Wednesday night was very cold, but we woke to sunshine and a world that was bright—a stark contrast to the gloomy day before. Though the university was officially closed, we judged that it was worthwhile getting there, so spent the afternoon at university. Next thing we know, it's Saturday and the weekend again!

   Ray ET. 2003. Learning XML. Cambridge, Mass.: O'Reilly
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 65,

Wikipedia—Set (Mathematics)
A Little Set Theory (Never Hurt Anybody) (pdf)

A Game of Thrones audiobook read by Roy Dotrice

Saving Grace—Oaxaca music video

Thursday, 7 June 2012

QEII's Diamond Jubilee

Queen Elizabeth II
Her Majesty, Queen Elizabeth II. Image courtesy of the Governor General of New Zealand. License: Copyright held by the Royal Household

Along with the rest of her subjects, The Praise of Insects celebrates 60 years of benevolent rule by Her Majesty Queen Elizabeth II.

Only 4 more years before she's beaten Vicky's record. Long live the Queen!

Tuesday, 5 June 2012

Checklist of Australian Weevils

Acantholophus cf. tragocephalus
Acantholophus, a member of the exclusively Australian tribe Amycterini.
From the Barrow Island Biosecurity Image Database on PaDIL. License: CC: BY.

The Australian Faunal Directory has a brand new addition to its database of Australian animals—the weevils. The list to the 4061 weevil species of Australia, representing 829 genera, is now available online. Don't expect scintillating reading or pretty pictures at this stage though. The checklist is exactly that—a list of names. For some of us, however, these lists are very useful and the addition of the citation to the original description makes this particular checklist more useful still. It's a big job to create things like this, and I for one appreciate it greatly!

Saturday, 2 June 2012

PhD week 13: Dunedin

Mosgiels and the Taieri Plains
View overlooking Mosgiel and the Taieri Plains, Dunedin, New Zealand.

I spent the first few days of this week in Dunedin where I looked at specimens of Irenimus in the collection of my supervisor, Dr Barbara Barratt. She's worked on the group for many years, researching their ecology in Central Otago improved pasture, particularly focussing on the impact of parasitoid wasps introduced to control the pest weevils Argentine stem weevil and clover root weevil. As can be imagined, she's needed to know what shes' been looking at over the years, and to this end has amassed a collection of Irenimus which have been reliably identified by herself and others. It was important that I see this collection so that I can get an idea of what some of these species look like, and start building a framework of what things I think might be related to each other. The other purpose for my trip down there was to obtain specimens for DNA sequencing. Barbara and her team have done a lot of collecting throughout Central Otago, and have kept the results in ethanol. It's a whole lot easier for me to get specimens by looking through their collections, than going to each of the locations myself.

The trip down to Dunedin also nicely coincided with some tango workshops and milongas (social dance events) held by Dunedin Tango, making the entire trip successful from both academic and social perspectives.

   Cadge W. 2012. Possibilities and limits of medical science: Debates over double-blind clinical trials of intercessory prayer. Zygon 47(1): 43–64
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Leviticus 1–6, Psalms 63–64,

SeaView alignment program
The Daily Mash—Clarkson slammed for "owlist" rant