Articles by Samuel Brown

Loading all installed R packages

December 10, 2012 | Samuel Brown

The other day I was trying to set up an R for Windows installation on a USB drive. As I don't have a Windows machine, I had to use the university computer to do this task. However, for some reason, they've blocked R from downloading and installing pack... [Read more...]

An R function for finding coordinates of NZ localities

June 10, 2012 | Samuel Brown

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 ... [Read more...]

Alternate way of plotting means and errors

May 20, 2012 | Samuel Brown

Last month, I wrote a post discussing dynamite plots, noting that they're not considered to be especially good at presenting information. I got a little bit of flak for it, from people for and against dynamite plots. This post shows a different method of showing a point and an error ... [Read more...]

PhD week 7: Plotting and NIR spectroscopy

April 19, 2012 | Samuel Brown

Near-infrared (NIR) spectroscopy is a technique that measures the amount of heat absorbed or emitted by certain materials. It is used in a variety of applications, but in the agricultural world, it is often used to determine the quality and composition of mixed materials such as stock forage. It uses ... [Read more...]

Dynamite plots in R

April 6, 2012 | Samuel Brown

For some time I've contemplated creating a function for creating the dynamite plots beloved by many of the applied sciences. There's a lot of criticism regarding their utility, and there are several ways that present data in a more intelligible way. A search on the subject brings up pages with ... [Read more...]

Using Sweave with Beamer: A note on fonts

November 2, 2011 | Samuel Brown

Recently, I've been preparing a poster using the LaTeX packages Beamer and beamerposter. The poster discusses a bunch of R stuff that I've been doing lately, so I successfully used Sweave to incorporate R code into the poster. However, I had some troub... [Read more...]

Simplifying polygon shapefiles in R

April 19, 2011 | Samuel Brown

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 ... [Read more...]

Changing phylogeny tip labels in R

January 14, 2011 | Samuel Brown

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 ... [Read more...]

Canterbury Earthquakes part III

September 8, 2010 | Samuel Brown

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... [Read more...]

Canterbury Earthquakes part II

September 7, 2010 | Samuel Brown

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 ... [Read more...]

Less than negative?

September 6, 2010 | Samuel Brown

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] 1 2 3 4 5 6 7 8 9 10__ b[1] 4 5 6__ c[1] TRUE TRUE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE__ d[1] -1 -2 -3 -4 ... [Read more...]

Canterbury Earthquake

September 6, 2010 | Samuel Brown

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 ... [Read more...]

apply functions in R

August 31, 2010 | Samuel Brown

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... [Read more...]

Phylogenetic trees online

August 20, 2010 | Samuel Brown

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 ... [Read more...]
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