Publications by Samuel Brown
Less than negative?
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:ab3 & a<7] cd-7] > 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...
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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 happened last night, waking us up, and causing more damage to several buildings ar...
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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 country. This is incorrect, as earthquakes below magnitude 3 are extremely common and a...
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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...
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Two R functions for working with DNA alignments
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 functi...
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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 plott...
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Building R packages for Windows when you don’t use it.
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 download a nice, shiny .zip file to give to your mates. Problem solved. Related To l...
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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 wanted to display a number of one-line commands and output alternately. Looking up the fanc...
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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 trouble with package names that I wanted to typeset as small caps. The package names ...
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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 provides functions for conducting sliding window analyses on DNA sequences, the calculation of identi...
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