EpiWorkshop 2013: DNA methylation analysis in R

March 19, 2013
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Elemento Lab at Weill Cornell Medical College organized a workshop on Epigenomics. I had the opportunity to give a tutorial on DNA methylation analysis in R. The tutorial demonstrates how to analyze high-throughput bisulfite sequencing d...

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What’s New in 6.2: Open Source R 2.15.3

March 19, 2013
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by Thomas Dinsmore Last week, Revolution Analytics released the Limited Availability edition of Revolution R Enterprise Release 6.2. Interest in this new release is high, and we're very pleased with user response. Over the next several weeks, I will share more detailed information about the capabilities included in this new release. Revolution R Enterprise Release 6.2 supports open source...

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Learning-by-doing: my quest to master ggplot2 (part 1)

March 19, 2013
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Your browser does not support iframes.

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Veterinary Epidemiologic Research: GLM – Evaluating Logistic Regression Models (part 3)

March 19, 2013
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Veterinary Epidemiologic Research: GLM – Evaluating Logistic Regression Models (part 3)

Third part on logistic regression (first here, second here). Two steps in assessing the fit of the model: first is to determine if the model fits using summary measures of goodness of fit or by assessing the predictive ability of the model; second is to deterime if there’s any observations that do not fit the

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Dealing with different object types in a vector in R

March 19, 2013
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I came across a little problem while dealing with a vector in R which had one of the most simple solutions. These are, in my opinion, the most annoying problems with the most simple and commonsensical solution. Anyways, yet again Utkarsh comes to rescu...

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How not to reveal your MySQL DB login/password when sharing code on GitHub or BitBucket?

March 19, 2013
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Solution: use your ~/.my/cnfInside your ~/.my.cnf file define the connection parameters to your databases. For example, here I define two groups called local and toto:user = rootpassword = ultra_secrethost = localhostuser = capitaine_flamp...

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googleVis 0.4.2 with support for shiny released on CRAN

March 19, 2013
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The new version of googleVis 0.4.2 is now available via CRAN. Many thanks to all who provided feedback on version 0.4.0 and particularly to Sebastian Campbell, John Maindonald and Aonan Zhang. As usual, if you find any issues or bugs, please send us an email or add a line to our online issues log.With version...

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The evolution of EU legislation (graphed with ggplot2 and R)

March 19, 2013
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The evolution of EU legislation (graphed with ggplot2 and R)

During the last half century the European Union has adopted more than 100 000 pieces of legislation. In this presentation I look into the patterns of legislative adoption over time. I tried to create clear and engaging graphs that provide … Continue reading →

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Layman’s Random Forests

March 18, 2013
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I’m not a fan of the Top 40 style content on Quora, but a student in Dr. Leek’s Coursera class shared this absolute gem from Edwin Chen. I have not seen a better explanation: How do random forests work in layman’s terms? Suppose you’re very indecisive, so whenever you want to watch a movie, you ask

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Review of Mathematica 9 and R-link

March 18, 2013
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VIDEO TRANSCRIPT: Hello, this is Matt Asher from StatisticsBlog.com. I’m going to be reviewing Mathematica 9, from Wolfram Research. In particular, I’ll be focusing on using it with R and to do Monte Carlo simulations and other statistical work. You can find a full transcript of this video at my blog, including the source code

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One Pager Performance Report with knitr, R, and a Different Font

March 18, 2013
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Although I suffer from complete ignorance of typography, with a little help from a post from Hyndsight and post from mages' blog, I wanted to try a different font on the one-pager performance report that we created in Onepager Now with knitR. I do not think Open Sans Light is the best choice for this...

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R – Simple Recursive XML Parsing

March 18, 2013
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This is intended for those who are starting out in R and interested in parsing an XML document recursively. It uses DT Lang's XML package.If you want to just read certain types of nodes, then XPATH is great. This document by DT Lang is perfect for that...

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Baseball Statistics with R – Batting Average

March 18, 2013
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Baseball Statistics with R – Batting Average

I'm working on a new book about the R programming language. R is a language that is designed for use with statistics and data. I use it to analyze sports and social networking. I thought that it would be fun to write the book focusing on baseball statistics using data from Major League Baseball. This post...

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Replay of Revolution R Enterprise: 100% R and More

March 18, 2013
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If you missed last week's broadcast of the webinar Revolution R Enterprise: 100% R and More, I've embedded the replay below. If you're not familiar with the power, productivity and enterprise readiness that Revolution R Enterprise brings to open source R, this is a good place to start. Slides from the webinar and a downloadable video of the replay...

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RuPaul’s Drag Race season 5 predictions: episode 8

March 18, 2013
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RuPaul’s Drag Race season 5 predictions: episode 8

Wow, last week’s Drag Race post made the rounds in the stats and Drag Race circles. It was cross-posted to Jezebel and has been getting some pretty high-profile links. A little birdy told me that Ms. Ru herself has read it. I think I can die a happy man knowing that RuPaul has visited Bad… Continue reading →

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Geometric Random graphs

March 18, 2013
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Some days ago a friend of mine asked how much i knew about graph-theory. My answer: nothing. Anyway, i was able to read a little bit on Random Geometric graphs, so i came with this little function to help visualize these things: There are some pretty...

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Which political science journals will have a data policy?

March 18, 2013
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Which political science journals will have a data policy?

Making available replication materials for the research you do is A Good Thing. It’s also work, and it’s quite easy to never get around to. Certainly I claim no special virtue in this department so I am always happy when there’s an institutional stick to prod my better nature in the right direction. One such institutional

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Callback functions for GUI widgets

March 18, 2013
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Callback functions for GUI widgets

Of all the things I dislike about R, one of the biggest is the fact that you can declare a function within the list of arguments to another function. I’ve gotten over it for very minor operations needed by things like lapply, but it can drive me bonkers elsewhere. One such instance is writing an

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column-store R or: how i learned to stop worrying and love monetdb

March 18, 2013
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"Combining R's sophisticated calculations and MonetDB's excellent data access performance is a no-brainer. One gets the best of two (open source) worlds with minimal hassle." - Dr. Hannes Mühleisen"oh wow that was fast like a cheetah with a jetpack or something" - anthony damicowhy try monetdb + ra speed test of four analysis commands on sixty-seven million...

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Veterinary Epidemiologic Research: GLM – Logistic Regression (part 2)

March 17, 2013
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Veterinary Epidemiologic Research: GLM – Logistic Regression (part 2)

Second part on logistic regression (first one here). We used in the previous post a likelihood ratio test to compare a full and null model. The same can be done to compare a full and nested model to test the contribution of any subset of parameters: Interpretation of coefficients Note: Dohoo do not report the

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R, where should I start?

March 17, 2013
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This is a dynamic post which I will continue to update whenever I find something new. Hope you will find the following links useful.Online Courses for Learning the R languageTry R from Code Schoole-Books for Learning the R LanguageR for Beginners ...

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Comparing ESPN’s, CBS’s, and NFL.com’s Fantasy Football Projections using R

March 17, 2013
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Comparing ESPN’s, CBS’s, and NFL.com’s Fantasy Football Projections using R

In the future, we will determine how to select the best possible team by maximizing your team's projected points and minimizing its downside risk.  But in order to do this, we will have to rely on our best guess of how many points each player will score.  We will use 2012 projections from ESPN, CBS, and NFL.com and actual...

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Extracting Information From Objects Using Names()

March 17, 2013
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Extracting Information From Objects Using Names()

One of the big differences between a language like Stata compared to R is the ability in R to handle many different types of objects at once, and combine them together or pull them apart.  I had a post about objects last year, but I thought I'd sh...

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Mumbai, Mar 2013 – Portfolio Tutorial

March 17, 2013
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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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Variability of garch predictions

March 17, 2013
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Variability of garch predictions

How variable are garch predictions? Previously There have been several posts on garch, in particular: A practical introduction to garch modeling The components garch model in the rugarch package Both of these posts speak about the two common prediction targets: prediction (of volatility) at the individual times (usually days) term structure prediction — the average … Continue reading...

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Ordinal Data

March 17, 2013
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Ordinal Data

I expect to be getting some ordinal data, from 5 or 9 point rating scales, pretty soon, so I am having a look ahead how to treat those. Often ANOVA is used, even though it is well known not to be ideal fro a statistical point of view, so that is the st...

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Happy St Patrick’s Day

March 17, 2013
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Happy St Patrick’s Day

I love Saint Patrick’s Day for, at least, two reasons. The first one is that, on March 17th, you can play out loud The Pogues, the second one is that it’s the only day in the year when I really enjoy getting a Guiness in a pub. And Guiness is important in statistical science (I did mention a couple...

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caretEnsemble Classification example

March 16, 2013
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caretEnsemble Classification example

Here's a quick demo of how to fit a binary classification model with caretEnsemble.  Please note that I haven't spent as much time debugging caretEnsemble for classification models, so there's probably more bugs than my last post.  ...

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Blend what?

March 16, 2013
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Why?Over the years I have learned quite a few things about machine learning but I have never thought of writing them down properly. Too often I can't figure out exactly what I did when I look at my old codes. The time is NOW!More importantly, I have fa...

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