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...
Blog Archives
SPIDER makes the top 10 barcoding publications of 2012
In the recent Barcode Bulletin published by iBoL, our humble paper announcing the R package spider: Species identity and evolution made second on their list of the top 10 publications of 2012. Not bad for a side project! Spider is available for downl...
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....
Alternate way of plotting means and errors
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 bar. If you're going to do it, why...
PhD week 7: Plotting and NIR spectroscopy
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 electromagnetic radiation...
Dynamite plots in R
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 such emotive titles as "Dynamite plots: unmitigated evil?"...
Interactive function for distances in plots
The following R function returns the distance between two points located on a plot. The distance returned is in the same units as that of the plot.
interDist aa dx dy sqrt(sum(c(dx^2, dy^2)))
}
spider: an R package for species identity and evolution
spider: Species identity and evolution is an R package developed by the Lincoln University molecular ecology lab group to do a range of analyses that various lab members wanted to run that were not yet implemented in R. In particular, the package provi...
Using Sweave with Beamer: A note on fonts
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...
Alternately coloured line environment with fancyvrb
Recently, while typing up an R tutorial, I used the LaTeX fancyvrb package to create two environments—one coloured blue for R commands, and one coloured red to display R output. This worked well for large blocks of each type. Then I decided I wan...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
