Blog Archives

Building R packages for Windows when you don’t use it.

May 2, 2011
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Are you a non-windows user wanting to share your R package with others who do use windows? There's a handy utility (http://win-builder.r-project.org/)that allows you to upload your .tar.gz file and it checks it, builds it, and sends you a link to downl...

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Simplifying polygon shapefiles in R

April 19, 2011
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Simplifying polygon shapefiles in R

Recently I downloaded the Crosby Code shapefile from Landcare Research's LRIS server for use in some publications I'm preparing. This shapefile is incredibly detailed, far more so than what I require. This detail means that it takes a while for the map to be plotted each time. As detail is less important for me than speed of...

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Two R functions for working with DNA alignments

March 28, 2011
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Recently I wrote a couple of small functions as a result of work done by myself and others in my lab group. The first is a function that determines what sites in a sequence alignment are ambiguous (i.e. not A, G, C or T). require(ape)data(woodmouse)is.ambig    x    bases    ambig    ambig > 0}is.ambig(woodmouse)This function utilises the bit-level coding scheme that...

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Changing phylogeny tip labels in R

January 14, 2011
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Changing phylogeny tip labels in R

During the process of molecular systematic research, specimens are given code names and numbers to keep track of data through the pipeline. These can contain a lot of information of relevance to the researcher, but unfortunately are meaningless to others who aren't as involved with the data. On publication, it is necessary to change the names from the code...

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Canterbury Earthquakes part III

September 8, 2010
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Canterbury Earthquakes part III

As more people keep following the GeoNet website, they are starting to notice the seismic activity in areas other than Christchurch. A few people I've talked to have expressed concern that the Saturday 7-pointer has sparked earthquakes around the count...

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Canterbury Earthquakes part II

September 7, 2010
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Canterbury Earthquakes part II

Since posting last night, there's been several more aftershocks, including several big ones. The total now stands (at 7:00pm) at 304 aftershocks, 70 greater than 4 on the Richter scale, 29 greater than 4.5, and 10 greater than 5. A couple of the fives ...

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Less than negative?

September 6, 2010
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An interesting thing that I found while doing the analysis for my previous post on the Canterbury earthquakes, was the difficulty of constraining figures less than a negative number. For example:abcd> a 1 2 3 4 5 6 7 8 9 10> b 4 5 6> c TRUE...

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Canterbury Earthquake

September 6, 2010
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Canterbury Earthquake

4:35 am on Saturday morning, I was woken up by a 7.1 magnitude earthquake, the epicentre being approximately 30 km west of where I live in Christchurch, New Zealand. The earthquake was one of the largest that New Zealand has experienced, and has been the most destructive one since the earthquake that struck Napier in 1931. Thankfully, the...

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apply functions in R

August 31, 2010
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Getting to know the "apply"s in R is extremely handy for using the language efficiently and effectively. Unfortunately, the help files tend to be rather information-dense and are fairly overwhelming for newcomers. A recent blog post by Neil Saunders pr...

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Phylogenetic trees online

August 20, 2010
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The other day, an article was published in PLoS One describing a newly developed JavaScript library to visualise phylogenetic trees online: jsPhyloSVG. It's pretty nifty, and there's some pretty cool functionality that you can build into the trees. It's all based on the PhyloXML standard for describing phylogenetic trees and networks, but can display trees...

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