Compiling RGDAL on OSX – Why do you hate me?

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.

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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:

  1. You need to have two data.frame objects to merge
  2. The first one in the function call will be the one merged on-to the second one is added to the first.
  3. 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.

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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.

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Compiling the GSL Library for OSX

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.

  1. It is easiest if you have XCode installed.  You can get this from the App Store for free.  Go download it and install it.
  2. Download the latest version of the GSL libraries.  You can grab them by:
    1. Looking for your nearest mirror site listed at http://www.gnu.org/prep/ftp.html and connecting to it.
    2. Open the directory gsl/ where all the versions will be listed.  Scroll down and grab gsl-latest.tar.gz.
  3. Open the terminal (Utilities -> Terminal.app) and type:  cd ~/Downloads
  4. Unpack the archive by:  tar zxvf gsl-latest.tar.gz then cd gsl-1.16/ (or whatever the version actually was, it will probably be some number larger than 1.16).
  5. Inside that folder will be a README file (which you probably won’t read) and an INSTALL file (which you should read).  In that folder it will tell you to:  ./configure then  make then sudo make install. This last command will require you to type in your password as it is going to install something into the base system.
  6. All the libraries and header files will be installed into the /usr/local/ directory.
Dyer RJ. 2015  Is there such a thing as landscape genetics?  Molecular Ecology.

Dyer RJ. 2015 Is there such a thing as landscape genetics? Molecular Ecology.

For a scientific discipline to be interdisciplinary it must satisfy two conditions; it must consist of contributions from at least two existing disciplines and it must be able to provide insights, through this interaction, that neither progenitor discipline could address. In this paper, I examine the complete body of peer-reviewed literature self-identified as landscape genetics using the statistical approaches of text mining and natural language processing. The goal here is to quantify the kinds of questions being addressed in landscape genetic studies, the ways in which questions are evaluated mechanistically, and how they are differentiated from the progenitor disciplines of landscape ecology and population genetics. I then circumscribe the main factions within published landscape genetic papers examining the extent to which emergent questions are being addressed and highlighting a deep bifurcation between existing individual- and population-based approaches. I close by providing some suggestions on where theoretical and analytical work is needed if landscape genetics is to serve as a real bridge connecting evolution and ecology sensu lato.

DOI http://dx.doi.org/10.1111/mec.13249

Install rgeos on OSX

There seems to be some nefarious conspiracy against packaging spatial R packages on the mac platform. Don’t quite understand it but it sucks.  Here is how to install the rgeos package.

If you try the normal way, you get the following error:

which is not very helpful.   Read more

Color palettes in ggpairs

Working on some code and was having a tough time configuring the color palette in GGally since it does not produce a ggplot object.  It appears to be a larger problem.  So, here is one hack, redefine the ggplot function and change the default palette there.  Need to make a dyerlab::palette now…