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)…