GEO database: curation lagging behind submission?

August 30, 2010
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GEO database: curation lagging behind submission?

I was reading an old post that describes GEOmetadb, a downloadable database containing metadata from the GEO database. We had a brief discussion in the comments about the growth in GSE records (user-submitted) versus GDS records (curated datasets) over time. Below, some quick and dirty R code to examine the issue, using the Bioconductor GEOmetadb

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MCMC Diagnostics in R with the coda Package

August 29, 2010
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MCMC Diagnostics in R with the coda Package

This is a follow up to my recent post introducing the use of JAGS in R through the rjags package. In the comments on that post, Bernd Weiss encouraged me to write a short addendum that describes diagnostic functions that you should use to assess the output from an MCMC sampler. I’ve only been using

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Beta translation done!

August 29, 2010
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Beta translation done!

Once my team of four translators had handed back to me all the chapters of the French version of Introducing Monte Carlo Methods with R to me, I had to go over the book to ensure some minimal consistency between the chapters. I started the editing in the plane to Vancouver but did not get

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SST with Raster. Complete

August 29, 2010
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SST with Raster. Complete

Update: new zip, correcting bug found by Steve  McIntyre: if(!file.exists(HadSST2ncdf)) downloadHADSST2() if(!file.exists(HadSST2ncdf)) downloadHadSST2() issue pending with another line as well. Checking raster versions. I’ve also, added some code into “downloadHadSST2″ that corrects for the “NA” problem with HadSST. (currently commented out). There is an issue with “ncdf” handling CF standards, which has been addressed in

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Subset views in R

August 28, 2010
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Subset views in R

I don’t know how to do this in R. So let me just say why I can’t. I wanted something akin to Boost‘s sub-matrix views, where you can have indexes map back to the original matrix, so you don’t create … Continue reading →

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Blegging for Data

August 28, 2010
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I’m in the middle of a new project that involves analyzing the packages that are currently on CRAN. As part of my work, I could really benefit from information about which packages are installed on people’s computers. If you’re willing to part with a bit of your time and privacy, I’d very much appreciate you

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Patrick Burns is blogging

August 28, 2010
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Patrick Burns is blogging

Patrick Burns is the author of several helpful R resources, including A Guide for the Unwilling S User, The R Inferno, and S Poetry. He also wrote one of my favorite critiques of Microsoft Excel: Spreadsheet Addiction. His writing is witty, entertain...

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Mike’s CNC 2010-08-27 18:36:00

August 27, 2010
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Support the OpenGov idea to create a "Platform for number crunchers across (US Federal) government" HERE. A small team is building a small pilot and I'm happy to report that R appears on many of the posts. If you like the idea (or even if you don't),...

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Mike’s CNC 2010-08-27 18:36:00

August 27, 2010
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Support the OpenGov idea to create a "Platform for number crunchers across (US Federal) government" HERE. A small team is building a small pilot and I'm happy to report that R appears on many of the posts. If you like the idea (or even if you don't),...

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Fractals in R

August 27, 2010
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Fractals in R

Atte Tenkanen had a blog on fractals using R for a time. Much of his source code is still available online.  To produce his version of the Mandelbrot set:source('http://users.utu.fi/attenka/mandelbrot_set.R')Fractals (such...

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Fractals in R

August 27, 2010
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Fractals in R

Atte Tenkanen had a blog on fractals using R for a time. Much of his source code is still available online.  To produce his version of the Mandelbrot set:source('http://users.utu.fi/attenka/mandelbrot_set.R')Fractals (such...

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Because it’s Friday: How Machines Work

August 27, 2010
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Because it’s Friday: How Machines Work

Ever wondered how a sewing machine seemingly manages to knot stitches without ever releasing the thread? Well, wonder no more: Find this and other animations of marvels of engineering, including the universal velocity joint and the rotary engine, at the link below. World Of Technology: Complicated Mechanisms Explained in simple animations (via) http://mytechnologyworld9.blogspot.com/2010/08/complicated-mechanisms-explained-in.html

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Poll: Half of SAS users considering a switch

August 27, 2010
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A recent poll of KD Nuggets readers suggests that of those using SAS today, almost half (49.6%) are considering switching to a different system for statistical analysis. The poll was prompted by the recent high court decision in the UK, that affirmed that "WPS is lawful clone of SAS system" (as stated in a WPS press release). The exact...

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Matlab-style multiple assignment in R

August 26, 2010
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Matlab-style multiple assignment in R

R again! You know how in Matlab you can do? S, I = sort(M) I like that. R generic functions makes this possible. First, let’s genericize assignment. I feel like regular “=” and “<-” oughta stay nongeneric, so let’s make … Continue reading →

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ProjectTemplate

August 26, 2010
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Introduction As many people already know, I’ve recently uploaded a new R package called ProjectTemplate to GitHub and CRAN. The ProjectTemplate package provides a function, create.project(), that automatically builds a directory for a new R project with a clean sub-directory structure and automatic data and library loading tools. My hope is that standardized data loading,

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Oh (de)bugger!

August 26, 2010
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Oh (de)bugger!

By number of questions asked, R passed MATLAB for the first time on Stack Overflow today. Thus it seems an appropriate time to write my first R-based post. This post concerns what to  do when your R-code goes pear shaped. Back in June there were a couple of very good videos on R debugging that

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New R User Groups in Seoul, Denver

August 26, 2010
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We have two new local R user groups to report this week. In Seoul, South Korea R user Chel Hee Lee is the organizer of the GNU R User's Group and Open Statistics Project in Korea. My translate-fu isn't quite up to figuring out when the next meeting is, but you can contact the group organizers here or here....

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Producing grids of plots in R with ggplot2: A journey of discovery

August 26, 2010
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Producing grids of plots in R with ggplot2: A journey of discovery

I’ve just gone through a bit of a ‘journey of discovery’ in R while trying to plot a grid of plots for one of the research projects I’m doing. I wanted to write a simple function which could produce this grid of plots from a CSV file, allowing me to easily view the trends of

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In Search of Power-laws: WikiLeaks Edition

August 26, 2010
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In Search of Power-laws: WikiLeaks Edition

Yesterday, a commenter reminded me of the very popular hobby among scientists of searching for power-law distributions in large event data. While the commonality of scale invariance in event data is quite well known—particularly with respect to conflict data—this has not prevented many researchers from seeking and finding these patterns in data. As the commenter notes,

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Mike’s CNC 2010-08-26 06:37:00

August 26, 2010
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Rweblinks, by Abhijit: http://files.meetup.com/1503964/Rweblinks.html.

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Mike’s CNC 2010-08-26 06:37:00

August 26, 2010
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Rweblinks, by Abhijit: http://files.meetup.com/1503964/Rweblinks.html.

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Louis: A Silent Film with Live Music

August 26, 2010
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The Chicago Symphony hosted the world premiere of Louis last evening, and I had snatched the (literally) last available ticket. The film, which is written, directed and producted by Dan Pritzker, is based loosely on the early years of Louis Armstro...

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Labor vote share across different types of balloting

August 26, 2010
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Labor vote share across different types of balloting

We’re starting to get more divisions reporting two-candidate preferred numbers by vote type. The emerging picture (literally) is one in which Labor’s performance on the pre-polls and postals is lagging its performance in ordinary votes. On the other hand, Labor seems to be doing well among absentee voters (the regression line sitting above the 45

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Global Temperature Proxy Reconstructions ~ now with CO2 forcing

August 26, 2010
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Global Temperature Proxy Reconstructions ~ now with CO2 forcing

Previously, I did a simple Bayesian projection of recent temperature using proxy data and the methods shown in McShane and Wyner (2010). I showed that when you take out the last 30 years of data (1969~1998), the projection does not track the recent uptick in temperatures well. The “projection” is a simple unparametric bootstrap which

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Online Certificate Courses in Computational Finance with R

August 25, 2010
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As announced on the R-Sig-Finance mailing list, the University of Washington is now offering a three-course online certificate in computational finance, using the R programming language as the software base. The three courses are: Investment Science R Computing for Computational Finance Portfolio Construction and Risk Management The course is presented by Doug Martin (founder of S-PLUS and longtime computational...

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Excel Errors and Other Numerical Nightmares

August 25, 2010
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Excel Errors and Other Numerical Nightmares

Although I use Excel all the time, and I strongly encourage my students to use it for performance analysis and CaP, I was forced to include a warranty disclaimer in my GCaP book because I discovered a serious numerical error while writing Appendix B. There, my intention was just to show that Excel gives essentially the same results...

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Excel Errors and Other Numerical Nightmares

August 25, 2010
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Excel Errors and Other Numerical Nightmares

Although I use Excel all the time, and I strongly encourage my students to use it for performance analysis and CaP, I was forced to include a warranty disclaimer in my GCaP book because I discovered a serious numerical error while writing Appendix B. There, my intention was just to show that Excel gives essentially the same results...

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Slides and replay for “Big Data with Revolution R”

August 25, 2010
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Thanks to everyone who attended our webinar this morning, Big Data Analysis for R Using Revolution R Enterprise, and in particular thanks for all the thoughtful questions during the Q&A session. If you missed the live broadcast, a replay is now available (requires the ability to view WMV files), and you can also download the slides in PDF format....

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Creating a Presentation with LaTeX Beamer – Using Overlays

August 25, 2010
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Creating a Presentation with LaTeX Beamer – Using Overlays

Overlays can be used in a LaTeX beamer presentation to reveal parts of a slide sequentially, which can be a useful way of imparting information to your audience. There are a number of different ways that overlays can be created depending on the sophistication required in the presentation. Fast Tube by Casper The \pause command is the

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