ggplot2: Crayola Crayon Colours

January 21, 2010
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ggplot2: Crayola Crayon Colours

Statistical Algorithms blog attempted to recreate a graph depicting the growing colour selection of Crayola crayons in ggplot2 (original graph below via FlowingData). He also asked the following questions: Is there an easier way to do this? How can I make the axes more like the original? What about the white lines between boxes and

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Scheduled Parallel Computing with R: R + Rmpi + OpenMPI + Sun Grid Engine (SGE)

January 20, 2010
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Recently I’ve learned how to do parallel computing in R on a cluster of machines thanks to the R packages snowfall, snow, and Rmpi. I’ve been using the SOCKET method with snowfall since together they make things simple. With these tools, I can reduce day/week long jobs to hours or a day across many (100)

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Remote download and viewing of brain atlas

January 20, 2010
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Remote download and viewing of brain atlas

The dcemriS4 package allows one to easily import and display NIfTI-1 class data sets. The following code takes the MNI152 brain atlas from the WWW and produces an orthographic display using the mid-axial, mid-sagittal and mid-coronal planes.

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Remote download and viewing of brain atlas

January 20, 2010
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Remote download and viewing of brain atlas

The dcemriS4 package allows one to easily import and display NIfTI-1 class data sets. The following code takes the MNI152 brain atlas from the WWW and produces an orthographic display using the mid-axial, mid-sagittal and mid-coronal planes.

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How to integrate R into web-based applications (video)

January 20, 2010
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The slides and videos from Jeff Horner's talk at last week's Bay Area User Group session on R-Powered Web Apps are now available. I've embedded it here below, but you might want to click through to larger size for better readability on the slides. Jeff's talk (titled "Use Rapache! It works") gives an overview of how to integrate R...

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RClimate Script: CO2 Trends

January 20, 2010
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RClimate Script: CO2 Trends

This RClimate Script lets users retrieve the latest data file on monthly Mauna Loa  CO2 levels and generate a trend chart with the latest reading highlighted. CO2 Trends – Keeling Curve Here’s the Mauna Loa Observatory CO2 trend from 1958 to Dec., 2009. Here are the data and RClimate Script links: Data Link RClimate Script link Posted in

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GWAS Manhattan plots and QQ plots using ggplot2 in R

January 20, 2010
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Will posted earlier this week about how to produce manhattan plots of GWAS results using Stata, so I thought I'd share how I do this in R using ggplot2. First, if you've never used ggplot2, you'll need to add it to your R installation by typing: install.packages("ggplot2") Once you've done that, copy and paste this command to download the functions I wrote...

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Example 7.23: the Monty Hall problem

January 20, 2010
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Example 7.23: the Monty Hall problem

The Monty Hall problem illustrates a simple setting where intuition often leads to a solution different from formal reasoning. The situation is based on the game show Let's Make a Deal. First, Monty puts a prize behind one of three doors. Then the player chooses a door. Next, (without moving the pize) Monty opens an...

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New UseR group in Seattle, WA

January 19, 2010
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There's a new local R user group to add to the list. The latest addition is in Seattle, WA and the first meeting of the Seattle useR Group is tomorrow. The group is organized by Zack Stednick (a data analyst and R user at the Fred Hutchinson Cancer Research Center in Seattle), and this meeting is hosted by my...

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Introduce your friends to R

January 19, 2010
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R has gotten quite a lot of exposure recently. It started with the feature article in the New York Times last January, but since then there's been a steady flow of articles about R in analyst reports, on blogs, in YouTube videos, on Twitter, as well as in the general news media. As a result, a lot of new...

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Solution manual for Introducing Monte Carlo Methods with R

January 19, 2010
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Solution manual for Introducing Monte Carlo Methods with R

After the complete solution manual for Bayesian Core, the solution manual for the odd numbered exercises of “Introducing Monte Carlo Methods with R” is now arXived. The fuller 133 page version for instructors is available from Springer Verlag by demand only, in order to keep the appeal of the book as a textbook (even

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Use Rapache: It Works!

January 18, 2010
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Presentations given at the Bay Area useR Group on January 10, 2010 by Jeff Horner, creator of the Rapache module, on "R-driven web applications".

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New features in ggplot2 version 0.85

January 18, 2010
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Hadley Wickham recently updated the ggplot2 package for R to version 0.8.5. In addition to bugfixes and performance improvements, this version introduces some handy new features. Among them: the ability to display mathematical equations as text, automatic legends for color scales, and user-configurable axis labels and legend titles. The Learning R blog runs through the new features with worked...

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Coming to R from SQL, Python, SAS, Matlab, or Lisp

January 18, 2010
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Head over to Revolutions Blog for a list of PDF and powerpoint resources for making the transition to R from other programming or stats languages.  All of these notes come from the New York R meetup. I enjoyed browsing the meetup's files - lots of powerpoints, PDFs, and example R data files for various topics, including several slideshows on...

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Updates to SoilWeb

January 17, 2010
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Updates to SoilWeb

Soil Profiles in Color Added color support to the mini-profiles used in graphical map unit summaries, the Google Earth interface, and iPhone application. SSURGO doesn't contain soil color data, so colors (in Munsell notation) were extracted from the OSD database, and...

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Donate to the R Video Hosting Fund

January 17, 2010
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Today I finished uploading a couple new talks to the growing repository of online presentations from the NYC R Statistical Meetup. Going forward, my plan is—whenever possible—to make all talks and presentation materials available online, in an effort to reach as wide an audience as possible. Our volunteer speakers bring immense expertise to these

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MATLAB/R Dictionary (Rosetta Stone Talk – 1/3)

January 17, 2010
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Presentation given by Harlan Harris at the NYC R Statistical Meetup on January 7, 2010. The January Meetup was the "R Rosetta Stone," and this talk covers R and MATLAB.

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Data munging with SQL and R (Rosetta Stone Talk – 3/3)

January 17, 2010
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Presentation given by Josh Reich at the NYC R Statistical Meetup on January 7, 2010. The January Meetup was the "R Rosetta Stone," and this talk covers R, SQL and Postgres.

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Typos in Chapter 8

January 16, 2010
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Typos in Chapter 8

Phew!, we are now done with the solution manual in the sense that we have compiled solutions for all odd-numberedd exercises (but one!) and solved a fair number of even-numbered exercises. As it stands, the manual is 120 pages long and I am exhausted by the run to produce it over the past week. I

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Getting Started with the R Programming Language

January 16, 2010
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Download Code Like A Pirate - The #rstats Appliance from the SUSE Gallery  The R programming language was featured about a year ago in a New York Times article (http://bit.ly/iaqQ). I've been an R user since 2000, so I've collected some resources ...

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Connecting to a DB2 database from R

January 16, 2010
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Connecting to a DB2 database from R

Unlike RMySQL and RSQLite there is no RDB2. However, I found it pretty straightforward connecting to a DB2 database using the JDBC driver and the RJDBC package. For all this to work, DB2 should be setup to use TCPIP, which is not used by default. You need to set the DB2COMM DB2 environment variable to

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Interesting use of levelplot() for time series data

January 16, 2010
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Interesting use of levelplot() for time series data

levelplot example: soil temperature (left) and moisture (right) Several recent articles appeared on the R-bloggers feed aggregator that demonstrated an interesting visualization of time series data using color. This style of visualization was readily adapted for the time...

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Gay Marriage: Another Data Point

January 16, 2010
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Relevant to my earlier post about the relationship between direct democracy and laws prohibiting gay marriage, Pew Research just published poll data showing that a majority of Americans disapprove of same-sex marriage.

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A tale of two visualizations (because it’s Friday)

January 15, 2010
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A tale of two visualizations (because it’s Friday)

GEEK FIGHT!!! says JD Long on Twitter as the New York Times publishes a widely-reposted interactive graphic about Netflix rental data, and the Wall Street Journal also gets into the interactive-viz game with a graphic on bank bonuses. If it's a fight, it's a knockout in the first round, if you ask me. There's no surprise why the Netflix...

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Equivalents to SAS, SPSS modules in R

January 15, 2010
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Bob Muenchen, the author of R for SAS and SPSS Users, has created a handy table listing the R packages that implement the statistical methods included in add-on modules for SAS and SPSS. For example, if you're looking for the equivalent structural equation modeling functions you might be using in PROC CALIS from SAS/STAT or the SPSS "Amos" software,...

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R Tutorial Series: Hierarchical Linear Regression

January 15, 2010
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R Tutorial Series: Hierarchical Linear Regression

Regression models can become increasingly complex as more variables are included in an analysis. Furthermore, they can become exceedingly convoluted when things such as polynomials and interactions are explored. Thankfully, once the potential independe...

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Learning R via Python…or the other way around (Rosetta Stone Talk – 2/3)

January 15, 2010
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Presentation given by Drew Conway at the NYC R Statistical Meetup on January 7, 2010. The January Meetup was the "R Rosetta Stone," and this talk covers R and Python.

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RQuantLib 0.3.2 released

January 14, 2010
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A new version of RQuantLib (a package combining the quantitative analytics of QuantLib with the R statistical computing environment and language) is now out at CRAN and in Debian (where it depends on the 1.0.0 beta of QuantLib that is currently in t...

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RQuantLib 0.3.2 released

January 14, 2010
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A new version of RQuantLib (a package combining the quantitative analytics of QuantLib with the R statistical computing environment and language) is now out at CRAN and in Debian (where it depends on the 1.0.0 beta of QuantLib that is currently in the ...

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