Monthly Archives: March 2013

The options mechanism in R

March 2, 2013
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Customization in R. Basics Several features benefit from being customizable — either because of personal taste or specifics of the environment. The way R implements this flexibility is through the options function.  This both sets and reports options.  For example, we can see the names of the options that are set by default: > names(options()) The post The...

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making a random walk geometrically ergodic

March 1, 2013
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making a random walk geometrically ergodic

While a random walk Metropolis-Hastings algorithm cannot be uniformly ergodic in a general setting (Mengersen and Tweedie, AoS, 1996), because it needs more energy to leave far away starting points, it can be geometrically ergodic depending on the target (and the proposal). In a recent Annals of Statistics paper, Leif Johnson and Charlie Geyer designed

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Tools for making a paper

March 1, 2013
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Since it seems to be the fashion, here’s a post about how I make my academic papers. Actually, who am I trying to kid? This is also about how I make slides, letters, memos and “Back in 10 minutes” signs to pin on the door. Nevertheless it’s for making academic papers that I’m going to

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R 2.15.3 is released

March 1, 2013
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Follows is the announcement today from Peter Dalgaard, for the R Core Team: The build system rolled up R-2.15.3.tar.gz (codename “Security Blanket”) at 9:00 this morning. This is intended to be the final round-up release of the 2.15 series, and in fact of the entire 2.x.y series which started 2004-10-04. The list below details the changes in this release. You can get...

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Using ENCODE methylation data (RRBS) in R

March 1, 2013
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Using ENCODE methylation data (RRBS) in R

ENCODE project has generated reduced-representation bilsulfite sequencing data for multiple cell lines. The data is organized in an extended bed format with additional columns denoting % methylation and coverage per base. Luckily, this sort of generic...

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R 2.15.3 is released

March 1, 2013
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The final installment of the R 2.x series is now available: R 2.15.3 was released this morning. If you build R yourself, the source files can be downloaded from CRAN now; pre-built binaries for Windows, Mac and Linux will be available from the various CRAN mirrors over the next few days. This update mainly fixes a few minor bugs,...

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Counts may be ratio, but not importance

March 1, 2013
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I can see from those of you who have contacted me that there is still some confusion about the claims made by Sawtooth that MaxDiff estimates can be converted to ratio-scale probabilities.  Many of you seem to believe that if attribute A...

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Data Visualization: Shiny Spiced Consulting

March 1, 2013
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If you haven’t already heard, RStudio has developed an incredibly easy way to deploy R on the web with its Shiny Package. For those who have heard, this really isn’t new as bloggers have already been blogging about it for some … Continue reading → The post Data Visualization: Shiny Spiced Consulting appeared first on Data Community DC.

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Overlapping Histogram in R

March 1, 2013
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Overlapping Histogram in R

While preparing a class exercise involving the use of overlaying of histogram, I searched Google on possible article or discussion on the said topic. Luckily, I found a blog where the author demonstrated an R function to create an overlapping histogram...

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Using Rcpp with Boost.Regex for regular expression

March 1, 2013
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Using Rcpp with Boost.Regex for regular expression

Gabor asked about Rcpp use with regular expression libraries. This post shows a very simple example, based onone of the Boost.RegEx examples. We need to set linker options. This can be as simple as Sys.setenv("PKG_LIBS"="-lboost_regex") With that, the following example can be built: // cf www.boost.org/doc/libs/1_53_0/libs/regex/example/snippets/credit_card_example.cpp #include <Rcpp.h> #include <string> #include <boost/regex.hpp> bool validate_card_format(const std::string& s) { static const boost::regex e("(\\d{4}){3}\\d{4}"); ...

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