R Site Search with the ‘sos’ Package

December 15, 2009
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REvolution Computing is a sponsor of the Bay Area R User Group, which gathered on Tuesday for its monthly meeting. This month's meeting was in a cozy setting at San Jose State University, and was hosted by David Czerwinski who teaches data mining there. The topic at hand was search, and finding R packages to compliment the functionality requirements...

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Browse R Graphics with the R Graph Gallery and the R Graphical Manual

December 15, 2009
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One of R's biggest strengths is its unparalleled graphing capabilities.  Just see any of our previous posts on ggplot2, visualization, or other posts tagged with R. R has several fundamentally different systems for plotting, including base graphics, lattice, and ggplot2.  Furthermore, many add-on packages come with their own functions for producing problem-domain specific graphics. For example,

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R Tutorial Series: Graphic Analysis of Regression Assumptions

December 15, 2009
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R Tutorial Series: Graphic Analysis of Regression Assumptions

An important aspect of regression involves assessing the tenability of the assumptions upon which its analyses are based. This tutorial will explore how R can help one scrutinize the regression assumptions of a model via its residuals plot, normality h...

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Object-Oriented Programming in R: The Setter Methods

December 14, 2009
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With a little guidance from the indefatigable Hadley Wickham, I figured out today how to implement the setter methods that were missing from my example user class. To review, let’s rebuild the getter methods for my user object: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17

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NYT on breast cancer screening and probability

December 14, 2009
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The New York Times last weekend looked at the controversy around the recent changes to the mammogram guidelines from a mathematical perspective. Compared to the analysis based on Bayes' Theorem from the Harvard Social Science Statistics blog (which apparently caused some controversy itself: that post was deleted and later replaced after some errors apparently crept into the calculations), this...

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The Grammar of Graphics: ggplot2 package

December 14, 2009
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The grammar of graphics approach to constructing graphs has been implemented in the ggplot2 package in R. The author of the package, Hadley Wickham, has provided a website with many details of using the system to create nice looking graphics. The package removes many of the awkward parts of setting up graphical display that characterise other

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R 2.10.1 released

December 14, 2009
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The latest update to R, R 2.10.1, is now available for download in source form from your local CRAN mirror. Binary versions (for Mac, Windows, and Linux) will become available over the next few days. As a maintenance release, this update focuses on minor changes and bug fixes. The complete list of changes is available in the NEWS file,...

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Example 7.18: Displaying missing value categories in a table

December 14, 2009
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Example 7.18: Displaying missing value categories in a table

When displaying contingency tables (section 2.3.1), there are times when it is useful to either show or hide the missing data category. Both SAS and the typical R command default to displaying the table only for observations where both factors are observed.In this example, we generate some multinomial data (section 1.10.4) and then produce tables with and without...

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RQuantLib 0.3.1 released

December 13, 2009
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A new version of RQuantLib is now out at CRAN and in Debian. It updates the package to the 0.9.9 release of QuantLib and is mostly a maintenance release with a few minor fixes along the way. Full changelog details, examples and more details abo...

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RQuantLib 0.3.1 released

December 13, 2009
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A new version of RQuantLib is now out at CRAN and in Debian. It updates the package to the 0.9.9 release of QuantLib and is mostly a maintenance release with a few minor fixes along the way. Full changelog details, examples and more details about this...

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RQuantLib 0.3.1 released

December 13, 2009
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A new version of RQuantLib is now out at CRAN and in Debian. It updates the package to the 0.9.9 release of QuantLib and is mostly a maintenance release with a few minor fixes along the way. Full changelog details, examples and more details abo...

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Galton’s quincunx in R

December 13, 2009
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Galton’s quincunx in R

Andrej Blejec has a very nice R demo of Galton's quincunx (link1, link2). It is a bit tedious to copy the code from PDF to R console, but it is worth the effort as the demo simulation clearly shows the nature of quincunx. After a bit of search I also f...

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Galton’s quincunx in R

December 13, 2009
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Galton’s quincunx in R

Andrej Blejec has a very nice R demo of Galton's quincunx (link1, link2). It is a bit tedious to copy the code from PDF to R console, but it is worth the effort as the demo simulation clearly shows the nature of quincunx. After a bit of search I also f...

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CRU graph yet again (with R)

December 13, 2009
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CRU graph yet again (with R)

IowaHawk has a excellent article attempting to reproduce the infamous CRU climate graph using OpenOffice: Fables of the Reconstruction. We thought we would show how to produced similarly bad results using R. If the re-constructed technique is close to what was originally done then so many bad moves were taken that you can’t learn much Related posts:

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The Most Basic Elements of Object-Oriented Programming in R

December 13, 2009
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Until recently, I’ve never had any reason to learn how to define my own classes in R. Having learned this week, I was surprised to find out how easy it is to start implementing classes in R. If you know nothing about creating classes and class methods in R, here’s a very quick overview of

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Missing data imputation

December 12, 2009
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Missing data imputation

Probably all of us have met the issue of handling missing data, from the basic portfolio correlation matrix estimation, to advanced multiple factor analysis, how to impute missing data remains a hot topic. Missing data are unavoidable, and more encompassing than the ubiquitous association of the term, irgoring missing data will generally lead to biased estimates. The...

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A central hub for R bloggers

December 12, 2009
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A central hub for R bloggers

I would like to suggest to my readers to take a look and bookmark a new blog named R-bloggers which aims to be "a central hub of content collected from bloggers who write about R".It seems a nice idea to me to have a centralized source of information f...

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A central hub for R bloggers

December 12, 2009
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A central hub for R bloggers

I would like to suggest to my readers to take a look and bookmark a new blog named R-bloggers which aims to be "a central hub of content collected from bloggers who write about R".It seems a nice idea to me to have a centralized source of information f...

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Summarising data using bar charts

December 12, 2009
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Summarising data using bar charts

A bar graph is a frequently used type of display that compares counts, frequencies, totals or other summary measures for a series of categories, e.g. sales in different market sectors or in quarters in a financial year. The bar graph can be laid out with the categories either on the vertical or horizontal axis of

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Already a competitor?!

December 11, 2009
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Already a competitor?!

When looking around on Amazon, I found that “Introducing Monte Carlo Methods with R” was associated with another very recently published (same day as ours!) book, “Understanding Computational Bayesian Statistics“, by William Bolstad, that seems to mostly cover the same ground as us (with some connections with Bayesian Core for prior modelling in regression and

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new R package : bibtex

December 11, 2009
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I've pushed to CRAN the package bibtex package The package defines the read.bib function that reads a file in the bibtex format. The code is based on bibparse The read.bib function generates an object of class citationList, just like utils::citation

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Struggling with apply() in R

December 11, 2009
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Struggling with apply() in R

It’s common knowledge that I struggle wrapping my head around the apply functions in R. That is illustrated very clearly in the following discussion on Stack Overflow: Dirk’s comment is actually spot on. I’ve asked the same damn question at least 4-5 times. Only I didn’t really understand it was the same question. That’s one of

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Must-Have R Packages for Social Scientists

December 11, 2009
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Must-Have R Packages for Social Scientists

After recently having to think critically about the value of various R packages for social science research, I realized that others might find value in a post on “must-have” R packages for social scientists. After the immensely popular post on this topic for Python packages a follow-up seemed appropraite. If you conduct social

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R> if (done=TRUE) tweet me!

December 11, 2009
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R> if (done=TRUE) tweet me!

Let’s say that you’re fitting a cumbersome model so time is not to waste over a PC staring at the screen half anxious-half bored… Then, you can always leave and go on with meetings and all your daily routine and have R notify you the results! How? We will illustrate the situation above using some Bayesian Model

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Because it’s Friday: Detecting Cylons

December 11, 2009
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Because it’s Friday: Detecting Cylons

Battlestar Galactica (Ronald D Moore's reimagined version of the rather cheesy 70's sci-fi series) has been my favourite TV series (of any genre) of recent years, so I'm especially excited that Chris Bilder has given me the chance to blog about it. Chris, an Associate Professor in the Department of Statistics at the University of Nebraska-Lincoln, recently published an...

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A Lot of Deaths are Partly Self-Induced

December 11, 2009
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I’m a little surprised by Andrew Gelman’s post today, doubting the wisdom of a passage from Gary Becker’s work that reads: According to the economic approach, therefore, most (if not all!) deaths are to some extent “suicides” in the sense that they could have been postponed if more resources had been invested in prolonging life.

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Times Series Methods versus Recurrence Relations

December 10, 2009
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This term, I’ve been sitting in on Rene Carmona’s course on Modern Regression and Time Series Analysis. Much of the material on regression covered in the course was familiar to me already, but I’ve never felt that I had a real command of times series analysis methods. When Carmona defined the AR(p) model in class

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APIs: I wish the life sciences would learn from social networks

December 10, 2009
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APIs: I wish the life sciences would learn from social networks

I was prompted by a thread on the apparent decline of FriendFeed to look for evidence of declining participation in my networks. First, a quick and dirty Ruby script, tls.rb to grab the Life Scientists feed and count the likes and comments: #!/usr/bin/ruby require 'rubygems' require 'json/pure' require 'net/http' require 'open-uri' def format_date(d) if d

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Demography package

December 10, 2009
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Demography package

This package seems useful for demographers.

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