Publications by Jared Knowles
Geography and Data
The Economist recently ran a fascinating article about the emergence of geographical databases and their uses for presenting and analyzing data.All this has made it much easier to create maps that explain—at a glance—something that might otherwise require pages of tables or verbiage. “A percentage or a table is still abstract fo...
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Software for Surviving Graduate School Part 1
After introducing a colleague to the wonders of Dropbox today (more on that later) I realized that it might be useful to put out a list of software that is of use to graduate students. I often find that many of the software products I find indispensable are virtually unknown to many of my fellow graduate students. Certainly this is no...
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Scoping functions in R
I want to test embedding source code in the blog by using the handy Gist tool provided by GitHub. These two R functions are a good opportunity to test out embedding a Gist on the website. These functions allow for threshold testing within a vector in R, or over rows or columns of a dataframe as well as is shown at the end of the code. They are no...
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RStudio, BibTex, and LaTeX
I was having a little trouble getting RStudio to process BibTex entries and compile a LaTeX file. Bumping around on the great RStudio help forum, I found this entry, which pointed me in the direction. I needed to set a system environment variable in R to let RStudio and R know where to look for the proper BibTex style, LaTeX input, and BIB input ...
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All Your Source Code Are Belong to… Nature?
The Journal of Nature put out an interesting op-ed recently discussing the need to make source code available for scientific articles that require statistical computation to produce their results. http://www.nature.com/nature/journal/v482/n7386/full/nature10836.html The article is hits on a point that is absolutely critical–statis...
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R Tutorials and Learning Materials
We are getting ready to host an R bootcamp this summer at work and I am looking at building on materials that already exist. I just wanted to list a few here while I figure out the best ways to incorporate them. Video Tutorials:This is a fairly new resource, but now contains over 60 instructional videos that are two minutes or less for how to d...
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Making an Animated Heart GIF in R
Messing around with animations, I created this toy example to make a growing outline of a heart in R. I have put it up as a gist on GitHub and embedded it below. It uses the animation and the ggplot2 packages–both of which make it incredibly simple to make a good looking graphic. The formula to draw the hearts can be found thanks to Wolfram Ma...
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Sourcing an R Script from Dropbox
Working on my R bootcamp materials and I thought it would be handy to get the bootcamp computers setup by sourcing an R script that will install all necessary non-core packages in it. The problem? How to deploy this script efficiently. A quick method would be to simply source the script from a public Dropbox share. But, as the BioBucket points ou...
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Announcing eeptools
The LDS_TOOLS package for R has been replaced by the new eeptools package. I am renaming the package for a number of reasons. First, LDS is a technical industry term in education that stands for Longitudinal Data Systems, which is not commonly known and understood. Second, LDS_TOOLS is not a valid package name in CRAN as package names can only co...
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A Chlorpleth Map of Free and Reduced Price Lunch in R
Charles Blow has an excellent op-ed in the New York Times about public education this week. The most important point he makes is that the defunding of public education is coming at precisely the time when American school children are most vulnerable:Not only is our education system being starved of investment, but many of our children are literal...
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