The Johnson and Dyer laboratories have been funded by DEB-Evolutionary Ecology for the project, A landscape resistance mapping approach to understanding species invasion patterns. Congratulations to the gypsy moth crew.
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.
Why is it so hard to keep automated report centers up?
Here are my slides from a guest lecture I gave in ENVS 601. Interesting class, only place I’ve been called totally ignorant by another instructor… I’m thinking it was a compliment aimed at bias-free research approaches.
A previous visitor to the laboratory, Philip Bertrand, is taking a trip between his graduate programs to travel the world and report on climate change. Here is ongoing blog, cataloging their travel from across the globe. Definitely worth following.
Here is some interesting data coming out of the Baja Araptus attenuatus project. We looked at methylation variation, localized within the genome and compared the amount of among-population variation present. The underlying idea here is that in insects, methylation is more often encountered in coding regions, and has been shown in many cases to be influencing phenotype.
I am in various stages of writing technical texts using R/RStudio/knitr and have been looking for some methods that help in this process. My goals are to be able to:
- Maintain a single source tree that can produce the text (including graphics, statistical analyses, etc). easily
- Be able to produce high quality typesetting
- Be able to easily make epub
- Include both Code and output in the text.
I’ve just run across Gitbook and it looks like a good option, particularly with the help of the R package Rgitbook. Here is a bit of work that I had to do to get things going on my machine.
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.
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.
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.
# load in the raster library
Loading required package: raster
Loading required package: sp
Here is a map of the dogwood we’ve sampled in the Fan region of Richmond Virginia.
Here is a short (39 minute) video of some basic graphics approaches in R I use in a class on population genetics.
We have added a new member to our lab, Jane Remfert. She is an incoming ILS PhD Student who is going to work on pollen movement in dogwood. Very exciting!
Often there comes along a story that you see and think, “I would have been perfect for that study, why didn’t I think of that?” Here is another one.
Congratulations Dr. Chris Hittinger, this is awesome.
Two NSF grants submitted! Taking a bit of time out for some programming and to set up Dyerlab South (in the vicinity of 24.9515812,-80.5807652)…