methylKit: R package for DNA methylation analysis

December 21, 2011
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High-throughput bisulfite sequencing based methods are popular for measuring genome-wide DNA methylation levels. Here is an R package that helps with the analysis of such DNA methylation data. Although, it is still under heavy development current funct...

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Basics on Markov Chain (for parents)

December 20, 2011
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Basics on Markov Chain (for parents)

Markov chains is a very interesting and powerful tool. Especially for parents. Because if you think about it quickly, most of the games our kids are playing at are Markovian. For instance, snakes and ladders… It is extremely easy to write down the transition matrix, one just need to define all snakes and ladders. For the one above, we...

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Basics on Markov Chain (for parents)

December 20, 2011
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Basics on Markov Chain (for parents)

Markov chains is a very interesting and powerful tool. Especially for parents. Because if you think about it quickly, most of the games our kids are playing at are Markovian. For instance, snakes and ladders... It is extremely easy to write down th...

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Mortgage Refinance Calculator

December 20, 2011
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Mortgage Refinance Calculator

Mortgage rates are low, considering historical rates for the last 50 years. It may be timely to consider a mortgage refinance. The image above links to a simple tool for exploring mortgage refinance, built using rapache and the yet-to-be-archived yarr package for R. Hence, there are now two mortgage-related calculators on this site: MortCalc: A

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Simulating Confidence Intervals

December 20, 2011
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Simulating Confidence Intervals

As I am finishing up my thesis I have recently been plotting effects from many models. An important aspect of this is to show the uncertainty surrounding different estimates and effects. Following a paper by Gary King, Michael Tomz and Jason Wittenberg...

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Outliers in the European Parliament

December 20, 2011
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Outliers in the European Parliament

Earlier this year I had a lot of fun learning how to use the BeautifulSoup and mechanize modules in python to scrape websites. My goal was to scrape the European Parliament website for information on the activity levels of the different MEPs. I struggl...

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TikZ and R

December 20, 2011
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TikZ and R

TikZ is an awesome macro for producing beautiful graphics in LaTeX. I use it constantly as it has a very intuitive syntax, and it is easy to define global settings for your plots, ensuring that the graphics in your paper are all uniformly styled. One t...

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Simplifying Loops in R

December 20, 2011
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One of the things I do frequently in my research is the apply some function on a large number of rows in a data set. I am a great fan of the loop structure in R, and use this a lot. I know one should always vectorize and avoid loops in R, however for m...

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Review of ‘R in Action’ by Robert I. Kabacoff

December 20, 2011
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Review of ‘R in Action’ by Robert I. Kabacoff

By Joseph Rickert Yesterday, the cosmic randomizer placed me next to a newly minter lawyer in a crowed Los Gatos coffee shop. In three minutes of conversation I learned that that the fellow was interested in corporate law, was about to take a job that would give him a seat in the great VC/start-up game and that he had...

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I may have ventured into the first circle and Virgil Is NOT Here — Lehmann Primality Test in R

December 20, 2011
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So a post about Lehmann Primality Tests in HackerNews came across my twitter this morning. Seemed like a great quick coding exercise during lunch. Little Did I know…It is wonderfully simple primality test but i think i have hit up against some R quir...

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December 2011 issue of the R Journal: An overview

December 20, 2011
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December 2011 issue of the R Journal: An overview

The December 2011 issue of the R Journal is now available for download. Three times a year, the open-access journal of the R project publishes peer-reviewed articles on research and applications of R and R packages. As of the latest issue, all articles are published under a Creative Commons license, making them accessible for translation, academic and commercial uses...

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Assessing Model Fit Through Simulation

December 20, 2011
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Assessing Model Fit Through Simulation

In the area of political science where I am active (european politics) it is very common to simply estimate a model, and start drawing inferences immediately. This is a shame as drawing inferences from a model without assessing how well it fits the dat...

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Fast paced food-web plotting action

December 20, 2011
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Fast paced food-web plotting action

A simple foodwebOne of my interests is in food web topology and food web dynamics. My research in experimental ponds has left me with 2430 food webs to make sense of, and one way to facilitate understanding that many networks, and really any food web, is through visualization. There are...

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Pairs Trading Issues

December 20, 2011
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Pairs Trading Issues

(This article was first published on Eran Raviv » R, and kindly contributed to R-bloggers) A few words for those of you who are not familiar with the “pairs trading” concept. First you should understand that the movement of every stock is dominated not by the companies performance but by the general market movement. This is the origin of...

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Tutorial on SPARQL Package for R

December 19, 2011
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Tutorial on SPARQL Package for R

Tools are major enablers of Linked Science. One crucial aspect is how to access and analyze data, and especially how to get only that part of data which is of interest for a given research question.  Linked Data solves the … Continue reading →

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Rotational Trading Strategies: borrowing ideas from Engineering Returns

December 19, 2011
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Rotational Trading Strategies: borrowing ideas from Engineering Returns

Frank Hassler at Engineering Returns blog wrote an excellent article Rotational Trading: how to reduce trades and improve returns. The article presents four methods to reduce trades: Trade less frequently. I.e. weekly instead of daily rebalancing. Different criteria for enter / exit a trade. Smooth the rank over the last couple of bars. Combination of

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Visualizing ChaLearn Gestures Test Data

December 19, 2011
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Visualizing ChaLearn Gestures Test Data

The colored paths are labeled training data, just like in my last post on this.The title gives the "answer" for a test video:Could you tell from just this what the sequence of gestures was?Not perfectly, but way better than chance.See a couple more exa...

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RTextTools v1.3.2 Released

RTextTools was updated to version 1.3.2 today, adding support for n-gram token analysis, a faster maximum entropy algorithm, and numerous bug fixes. The source code has been synced with the Google Code repository, so please feel free to check out a copy and add your own features!With the core feature set of RTextTools finalized, the next major releas

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Blog Statistics with StatCounter & R

December 19, 2011
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Blog Statistics with StatCounter & R

If you're interested in analysing your blog's statistics this can easily be done with a web-service like StatCounter (free, only registration needed, quite extensive service) and with R.After implementing the StatCounter script in the html code of a we...

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IRIS Flower Data Set (R-003)

December 19, 2011
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IRIS Flower Data Set (R-003)

Centramos la matriz con el comando, generando a partir de A una nueva matriz que llamamos "Acentered"Acentered=scale(A,center=T)Ahora con la función "eigen":Esta es otra forma de proceder con el cálculo de los componentes principales (eigenvectors y ...

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Portfolio Optimization in R, Part 2

December 19, 2011
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Portfolio Optimization in R, Part 2

In the previous post, we built the efficient frontier of a portfolio of bonds. The next logical step is to find the super efficient (or market) portfolio holdings.  If you are unfamiliar with the concept, take a second and read the section section...

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Submit a paper to the R/Finance conference

December 19, 2011
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For anybody using the R language to analyze financial data, the R/Finance conference is the conference of the year. If you have something to share about applied finance with R, the call for papers is now open. The details are below, and the deadline for submissions is January 31, 2012. R/Finance 2012: Applied Finance with R May 11 and...

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Maximal Information Coefficient (MIC)

December 19, 2011
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Maximal Information Coefficient (MIC)

Pearson r correlation coefficients for various distributions of paired data (Credit: Denis Boigelot, Wikimedia Commons)A paper published this week in Science outlines a new statistic called the maximal information coefficient (MIC), which is able to equally describe the correlation between paired variables regardless of linear or nonlinear relationship. In...

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The R Journal (Volume 3/2, December 2011) is out

December 19, 2011
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The new R journal for December 2011 is out! You can Download the complete issue from here, while refereed articles may be downloaded individually using the links below: Table of Contents Editorial 3   Contributed Research Articles   Creating and Deploying an Application with (R)Excel and R  Thomas Baier, Erich Neuwirth and Michele De Meo 5 glm2: Fitting Generalized Linear Models...

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Christmas Gift to the R Community: The R Journal!

December 19, 2011
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Christmas Gift to the R Community: The R Journal!

The R Journal Volume 3/2 is available! Get it from here.

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Spatial Data with R

December 19, 2011
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Spatial Data with R

On September 14th 2011 Dr Alec Stephenson gave a talk on exploring spatial data with R (see Meetup page). The video of the talk is now available online. The talk provides a non-mathematical and entirely equation-free talk on visualizing and … Continue reading →

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data.frame objects in R (via “R in Action”)

December 18, 2011
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data.frame objects in R (via “R in Action”)

The followings introductory post is intended for new users of R.  It deals with R data frames: what they are, and how to create, view, and update them. This is a guest article by Dr. Robert I. Kabacoff, the founder of (one of) the first online R tutorials websites: Quick-R.  Kabacoff has recently published the book ”R Read more...

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Portfolio Optimization in R, Part 1

December 17, 2011
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Portfolio Optimization in R, Part 1

I briefly mentioned in my last post; that I was fooling around with portfolio optimization in R.  This post will the first in a series on the topic of portfolio optimization. Please note, nothing I am about to say should be taken as advice for investing.  These results are based on prior observed returns and the future...

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Function to Collect Geographic Coordinates for IP-Addresses

December 17, 2011
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Function to Collect Geographic Coordinates for IP-Addresses

I added the function IPtoXY to theBioBucket-Archives which collects geographic coordinates for IP-addresses.It uses a web-service at http://www.datasciencetoolkit.org// and works with the base R-packages. # System time to collect coordinates of 100 IP-...

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