Code

Cropping Rasters

It is often the case that the raster we are working with is not the exact size of the area from which our data are collected. It is a much easier situation if the raster is larger than the area than if you need to stitch together two raster Tiles to get all your data onto one extent. In my doctoral thesis work, the area of the southern Ozark mountains that my sites were in was not only straddling a boundary between existing rasters, it was also at the boundary of two UTM zones! What a pain.

Raster Plotting

A raster is essentially an image, whose pixel size correspond to a particular spatial extent and the data contained within each pixel represents a particular feature on the landscape. Common rasters are DEM’s (measuring elevation), rainfall, temperature, buildings, etc. In R, it is common to think of rasters as matrices whose values measure some feature on the landscape. In this section, we will examine how to acquire, load, manipulate, and extract data from raster objects.

Applied Population Genetics Textbook Release

I will be posting portions of all 10 chapters of my upcoming textbook, Applied Population Genetics, as early draft chapters to this website over the spring semester.

The Taxonomy of Academic Sustainability

Been working on a lexicographic analysis of ‘Sustainability’ as published by the journals PNAS and Sustainability. Here are the stemmed word forms for 366 published articles represented as a hierarchical clustering. The wordclouds represent the top 10 word stems per group.

Compiling RGDAL on OSX – Why do you hate me?

Every time I upgrade in any significant way, two R libraries seem to raise their ugly heads and scream like a spoiled child—rgdal and rgeos . Why do these two have to be SOOOO much of a pain? Why can’t we have a auto build of a binary with all the options in it for OSX? Who knows? I always feel like I get the fuzzy end of the lollipop with these two. Here is my latest approach for getting them going.

Merging data frames

In R, there is often the need to merge two data.frame objects (say one with individual samples and the other with population coordinates. The merge() function is a pretty awesome though it may take a little getting used to. Here are some things to remember: You need to have two data.frame objects to merge The first one in the function call will be the one merged _on-to _the second one is added to the first. Each will need a column to use as an index—it is a column that will be used to match rows of data. If they are the same column names then the function will do it automagically, if no common names are found in the names() of either data.frame objects, you can specify the columns using the optional by.x= and by.y= function arguments.

Loading in Rasters

Much of the work in my laboratory uses spatial data in some context. As such it is important to try to be able to grab and use spatial data to in an easy fashion. At present, R is probably the best way to grab, visualize, and analyze spatial data. For this example, I went to http://worldclim.org and downloaded the elevation (altitude) for tile 13 (eastern North America) as a GeoTiff. A GeoTiff is a specific type of image format that has spatial data contained within it. The tile data has a pixel resolution of 30 arc seconds which puts us in the general area of ~ 1km. First, we need to get things set up to work. # Set the working directory to where you want it. setwd("~/Downloads") # load in the raster library require(raster) Loading required package: raster Loading required package: sp

Basic graphics in R.

Here is a short (39 minute) video of some basic graphics approaches in R I use in a class on population genetics.

Installing R packages from github

The default CRAN repository is not the only place that R packages are stored. You can also find them on github. When I develop libraries for R, I typically develop them on http://github.com/dyerlab and then upload them to CRAN when I get to major milestones. The latest versions of all my software will always be found on github. So here is how to install packages directly.

Compiling the GSL Library for OSX

I’ve been working on integrating the Swift language into my analysis workflow but much of what I do involves the GNU Scientific Libraries for matrix analysis and other tools. Here is a quick tutorial on how to install the GSL library on a clean OSX platform.