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

PhD week 8: Structuring taxonomic descriptions

Biological taxonomy is the science of categorising the plants and animals that share this world with us. A critical part of this characterisation is the writing of a description detailing the features which (done well) allows others to identify members of the species in question. Traditionally, this is a piece of prose that is very technical and very dry to read. There is, however, a move towards standardising and atomizing descriptive information, to enable it to be more readily re-used for a variety of applications.

The first attempt at this was the DELTA format, which was drafted as early as 1975. This format is becoming somewhat dated, and efforts are being made to produce an XML-based standard, known as Structured Descriptive Data (SDD).

Computer programs that can be used to produce these structured datasets include LUCID, xper2 and Open DELTA. Somewhat more complex is the taxonomy editor produced by the European Distributed Insitute of Taxonomy, that appears to be the tool for populating their scratchpads.

For some fairly detailed commentary regarding the promises and challenges offered by this revolution in taxonomic data management, ZooKeys published a special issue on e-Infrastructures for data publishing in biodiversity science.

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Read:
   Wallis GP, Trewick SA. 2009. New Zealand phylogeography: evolution on a small continent. Molecular Ecology 18: 3548–3580
    Grant PR, Grant BR. 2008. How and Why Species Multiply. The Radiation of Darwin's Finches. Princeton: Princeton University Press
   McCulloch D. 2010. A History of Christianity: The First Three Thousand Years London: Penguin
   Psalms 44–47

Websites:
New Zealand's Geological Timescale
Importing DICOM images into Blender
3D slicer
ImageJ wiki

Watched:
Game of Thrones Season One

Asian Beetle Websites II

In addition to the websites on Asian beetles mentioned previously, here's a couple more which are worth visiting.

The first is the Kisti website that provides online access to issues of Insecta Koreana and the Journal of Asia-Pacific Entomology, both of which have many articles written in English. In addition they have issues of the Korean Journal of Applied Entomology and the Proceedings of the Korean Society of Applied Entomology Conference which are in Korean.

The second site is the insect collection database of the Kyushu University Museum (English page). Many of the database entries have got habitus photographs including the Acallinus tuberculatus shown above. Unfortunately, the encoding seems to be incompatible with my font set, which makes it look ugly and hard to navigate on my machine.

The fauna of the South Pacific at your fingertips....

That's right folks... PBIF now have a database up and running that allows you to find what specimens the Bishop Museum has in their hallowed vaults. It also has some nice pictures of parrotfish...

The insects, mammals, birds and fish all seem to be working well, though it seems to crash occasionally. No problem though - go away and come back, and all is good with the world again.

The general taxonomy database can be found here.