Monthly Archives: October 2012

Zurich, Aug 2012 – Swiss SBBI Data

October 7, 2012
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(This article was first published on Rmetrics blogs, and kindly contributed to R-bloggers) To leave a comment for the author, please follow the link and comment on their blog: Rmetrics blogs. R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave,...

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EDA Before CDA

October 6, 2012
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EDA Before CDA

One Paragraph Summary Always explore your data visually. Whatever specific hypothesis you have when you go out to collect data is likely to be worse than any of the hypotheses you’ll form after looking at just a few simple visualizations of that data. The most effective hypothesis testing framework in existence is the test of

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A quick introduction to ggplot()

October 5, 2012
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A quick introduction to ggplot()

I gave a short talk today to the about ggplot. This what I presented. Additional resources at the bottom of this post ggplot is an R package for data exploration and producing plots. It produces fantastic-looking graphics and allows one to slice and dice one’s data in many different ways. Comparing with base...

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Style your R charts like the Economist, Tableau … or XKCD

October 5, 2012
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Style your R charts like the Economist, Tableau … or XKCD

As we noted last month, the new Themes feature in ggplot2 helps you customize the design of R charts to your liking. Now, R user Jeffrey Arnold has built on this feature to create standardized themes to make R graphics looks like those from major publications and other software systems. You can use his ggthemes package to make your...

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How to read BSMAP methylation ratio files into R via methylKit

October 5, 2012
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BSMAP is an aligner for bisulfite sequencing reads. It outputs aligned reads as well as methylation ratios per base (via methratio.py script). The methylation ratios can be read into R via methylKit package and regular methylKit analysis can be performed using the BSMAP data.First,  you need to separate BSMAP methylation ratio file based on methylation context. Cs in CpG,...

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How to read BSMAP methylation ratio files into R via methylKit

October 5, 2012
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BSMAP is an aligner for bisulfite sequencing reads. It outputs aligned reads as well as methylation ratios per base (via methratio.py script). The methylation ratios can be read into R via methylKit package and regular methylKit analysis can ...

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DIY ZeroAccess GeoIP Plots

October 5, 2012
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DIY ZeroAccess GeoIP Plots

Since F-Secure was #spiffy enough to provide us with GeoIP data for mapping the scope of the ZeroAccess botnet, I thought that some aspiring infosec data scientists might want to see how to use something besides Google Maps & Google Earth to view the data. If you look at the CSV file, it’s formatted as

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Running motivation #An R amusement

October 5, 2012
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Running motivation #An R amusement

Henry John-Alder told me once that in a marathon, twice as runners cross the line at 2h 59m than at 3h 00m. He pointed out that this anomaly in the distribution of finishers per minute (roughly normal shaped) is due … Continue reading →

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Calculating distances (across matrices)

October 5, 2012
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Calculating distances (across matrices)

This Gist is mostly for my future self, as a reminder of how to find distances between each row in two different matrices. To create a distance matrix from a single matrix, the function dist(), from the stats package is sufficient. There are times, ho...

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How to upgrade R in Ubuntu 12.04

October 4, 2012
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Open your sources.list file in geditsudo gedit /etc/apt/sources.listand add the following line:deb http://cran.cnr.berkeley.edu/bin/linux/ubuntu/ precise/Note that you don't have to use that mirror. You may use any mirror from the list here : http://cran.r-project.org/mirrors.htmlAdd the secure APT key to your system with one commandsudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9Update your sources and upgrade your installationsudo apt-get update...

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