Turning In Assignments via Google Sharing

If you use Google Docs for your writing, there are several cool tricks you can use to increase your efficiency.  Here is one thing that has made it much easier when it comes to turning in assignments.  Previously, one would create a document in some word processor, work on it, put it on a thumb drive, take it home and work on it, take it back to school, perhaps a lab computer, maybe it is also worked on in the library, etc.  Eventually, you finish the document and then to turn it in you can either print it off (got to go find a printer or where I put that extra paper) or email it  in.  This last option is terrible if you have a large class!

If you are using Google Docs, you can just share it with the instructor.  In the sharing options, you can designate that you share with someone but only allow them to make “suggestions”.  This keeps the integrity of your document in place while allowing another person to mark it up.  Once you share it, they can open it and write in it but any and all changes to the document are indicated via a highlight color.  Since both of you are working on the document, there is no need to email it back and forth, there is only one document.

Here is a short video how that is done if you need more visual input.

Setting Up Your Site for Syndication

This quick tutorial is for how you set up your site to make it able to syndicate to a class site.  I am using the BIOL310 Genetics Online course as an example.  You are going to need the following:

  1. A category given to you by the professor to use on your site to indicate which posts should be sent over to the class site.
  2. A blog.  Here I am running WordPress as it is the supported one from VCU.  Others are available if you already have a blog going, if not got to rampages.us and sign up as a VCU student and make one.  Consider it a digital portfolio for all your work.
  3. Send your professor the address of your blog.

Below is a video of the process.  It is pretty easy to do.

That should be it. Once your professor has the link and sets up syndication, your posts (when the category is applied to them) will show up on the site.

GStudio: An R Package for Spatial Analysis of Marker Data

This is the main package that provides data types and routines for spatial analysis of genetic marker data. The previous version is currently available on CRAN and you can install it rom within your R environtment by invoking the command

install.packages("gstudio")

If you want to keep up with the latest developments of this package, you can use the version found on GitHub.  Install it from within R as:

require(devtools)
install_github("dyerlab/gstudio")

and that should get you up-to-date.  You’ll need to have a fully working LaTeX install and some other stuff to build it if you fork.

The Users Manual for the package with several examples can be found here

I have started a github account for this package, you can get access to the whole codebase read about it on the wiki, and contribute to the project from its repo at https://github.com/dyerlab.

Extracting Data from Rasters

This document shows you how to extract data from rasters.

 

Getting The Libraries

First, I’ll load in some packages to get the ability to work with raster data and to load in the Arapatus attenuatus data set (it is part of the default gstudiopackage).

 

Loading and Cropping Rasters

We can load in the raster, and then crop it to just the are we need. These rasters were downloaded from [http://www.worldclim.org] and are much larger than the study area. This just makes it easier on the computer to not have to deal with such large areas. After cropping it, we will load in the annual precip and temperature data as well.

 

Getting Example Data from Araptus attenuatus

Now, lets grab the Araptus data and look at the data and plot out the locations.

 

 

png-3

Extracting Point Data

To elevation, temperature and precipitation from the rasters for each sampling location, we need to translate them into points first. I’ll first grab the coordinate data as a data.frame.

 

Then we can grab them using the normal functions in the sp library.

 

 

Plotting Trend lines.

Cool, lets sort this by latitude

 

and then plot out some values to look at what is going on.

png

 

png-1

 

png-2

New digs

OQx70jjBSLOMI5ackhxm_urbex-ppc-030I’m moving the site from my own hand-coded html over to an instance of WordPress for 2015.  There are several reasons why I am doing this:

  1. I don’t seem to update too often if I hand code it making my lab webpage rather stale.
  2. Syndication and federation of posts can add dynamic content from lab members to the site.
  3. I’m moving towards this approach in teaching as well so I thought I would eat my own dogfood.

We will see how it goes.  Lots of stuff to add and go over.