R-ecap [-16]

March 26, 2011
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R-ecap [-16]

This morning, I noticed that none of my R related posts had appeared on R-bloggers for the past fortnight… After investigating, this was caused by…cut-and-paste! Indeed, when advertising about the special issue of TOMACS Arnaud Doucet and I edit about Monte Carlo methods in Statistics, I copied the main parts from the pdf announcement, straight

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clusterProfiler in Bioconductor 2.8

March 26, 2011
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In recently years, high-throughput experimental techniques such as microarray and mass spectrometry can identify many lists of genes and gene products. The most widely used strategy for high-throughput data analysis is to identify different gene clusters based on their expression profiles. Another commonly used approach is to annotate these genes to biological knowledge, such as Gene Ontology (GO) and...

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“An R package” or “A R package”

March 26, 2011
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“An R package” or “A R package”

I’m currently writing some lecture notes on R and I used the phrase “a R package” without thinking. Since the word following the article “a” was a consonant, I automatically went for “a” instead of “an”. The problem is that “R” sounds likes a vowel, so “a R package” grates on the listener. The correct

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solaR 0.22 is at CRAN

solaR 0.22 is at CRAN

The version 0.22 of solaR is now available at CRAN. Besides, solaR is now registered at R-Forge. A new mergesolaR method has been defined for merging solaR objects. The calculation of the sunset time has been improved. The voltage dependency of the efficiency curve of the inverter is now included in fProd and calcGCPV. The

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How to backtest a strategy in R

March 26, 2011
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This is the third post in the Backtesting in Excel and R series and it will show how to backtest a simple strategy in R.  It will follow the 4 steps Damian outlined in his post on how to backtest a simple strategy in Excel.Step 1: Get the dataThe ...

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How to backtest a strategy in R

March 26, 2011
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This is the third post in the Backtesting in Excel and R series and it will show how to backtest a simple strategy in R.  It will follow the 4 steps Damian outlined in his post on how to backtest a simple strategy in Excel.Step 1: Get the dataThe ...

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Le Monde puzzle [#7]

March 26, 2011
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Le Monde puzzle [#7]

The mathematical puzzle from the weekend edition of Le Monde from a few weeks ago was not too hard to solve by induction but my R code failed miserably! The puzzle was as follows: A calculator is broken in such a way that it starts by exhibiting 0, then pressing 4, 6 or 0 keeps

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A Request for Foursquare Data

March 25, 2011
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I’m trying to collect data sets that showcase how the classical statistical distributions appear in modern contexts. I’ve already got some data that shows how the gamma distribution appears in video game scores, and now I’m hoping to find an example where the exponential distribution

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Aquamacs 2.2 and ESS

March 25, 2011
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nStrict Standards: Non-static method StringParser_Node::destroyNode() should not be called statically, assuming $this from incompatible context in /afs/ir.stanford.edu/users/k/n/knoepfle/cgi-bin/flatpress/fp-plugins/bbcode/inc/stringparser.class.php o...

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Aquamacs 2.2 and ESS

March 25, 2011
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News of the latest release of Aquamacs, version 2.2, appeared this week in my echo area. Given the opportunity to procrastinate, I dropped everything and upgraded; returning to work, I noticed that the version of ESS shipped with Aquamacs 2.2 is ESS 5...

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R inside Qt: A simple RInside application

March 25, 2011
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R inside Qt: A simple RInside application

The RInside package makes it pretty simple and straightforward to embed R, the wonderful statistical programming environment and language, inside of a C++ application. This uses both the robust embedding API provided by R itself, and the higher-level...

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Because it’s Friday: Do Celebrities Follow the Half Your Age Plus Seven Rule?

March 25, 2011
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celeb small

Remember the Dating Equation from a while back, that formula that determines the socially acceptable bounds for the age of a female companion given the age of the male partner? Well, the crack data analysis team at Revolution Analytics decided to take the 100 hottest celebrity couples of 2010, and create a scatterplot of the couple's ages (using R),...

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Loading CSV with Date and Time into Zoo in R

March 25, 2011
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Sometimes you are facing time series which has both date and time property in one column in CSV file. In this case you need to pass additional parameter into read.zoo function:   View Code RSPLUS1 z <- read.zoo("/path/to/file/test.csv&...

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Grey’s Anatomy Network of Sexual Relations

March 25, 2011
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This all began with an introductory presentation about social network analysis to a group of medical students.  What better way to grab their attention than with attractive, fake doctors having sex on television?  Naturally this led to the dense network … Continue reading →

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MCMC with errors

March 25, 2011
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MCMC with errors

I received this email last week from Ian Langmore, a postdoc in Columbia: I’m looking for literature on a subject and can’t find it:  I have a Metropolis sampler where the acceptance probability is evaluated with some error.  This error is not simply error in evaluation of the target density.  It occurs due to the

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Day #11 Easter “egg”

March 25, 2011
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This is not my daily blogpost, but something I found while searching for different plots just copy this code and post it in your Rserve (or what you use to give in R commands) install.packages("onion") require(onion) data(bunny) p3d(bunny,theta=3,phi=1...

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Radiation levels at Fukushima

March 24, 2011
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Radiation levels at Fukushima

From BWR The above graph is derived from data scraped from TEPCO press releases. Every hour or so for the first few days of the crisis, a TEPCO van would record radiation (probably Beta/Gamma, but the translation is unclear) at … Continue reading →

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No simulation is complete without a gif

March 24, 2011
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No simulation is complete without a gif

I promise this is my last post on the now week and a half old π pay! Building on the last post, I figured I could show how convergence actually works in the estimation algorithm. If you’ll recall, we plotted … Continue reading →

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Predicting R models with PMML: Revolution R Enterprise and ADAPA

March 24, 2011
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The recently announced Revolution Analytics / Zementis partnership goes a long way towards demonstrating how R fits into big-league production environments. A frequent complaint against R is that although R is fine prototyping tool it is not able to handle production environments. Well, that’s just not true. In fact, it is straightforward to build a model in R, translate...

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R Still On Top

March 24, 2011
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R Still On Top

According to the Google Ngram corpus, R is still the top rated statistical software package. Ok, I’m just kidding. That plot is worthless. All the data are from books published between the years 1890 and 2008, and none of those software packages wou...

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Silver Is A Weighted Coin

March 24, 2011
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Silver Is A Weighted Coin

editorial note: there is an error in the code explained below the code. When you flip a quarter, you normally assume the coin is fair and that there is a 50% chance of getting either heads or tails. Option pricing assumes the world of trading is f...

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Generate MP3 waveforms with Ruby and R

March 24, 2011
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Generate MP3 waveforms with Ruby and R

I blame Rully for this. If it wasn’t for him I wouldn’t have been obsessed with this and spent a good few hours at night figuring it out last week. It all started when Rully mentioned that he knew how many beeps there are in the Singapore MRT (subway system) ‘doors closing’ warning. There are

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Day #11 R graphs as nodes

March 24, 2011
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Today my company supervisor isn’t at work so he gave me (and the other students) a task-list. I have to check the availability of the following R scripts. Whether or not they work how they should in Knime. While doing these tasks, at the main tim...

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The Many Uses of Q-Q Plots

The Many Uses of Q-Q Plots

My last four posts have dealt with boxplots and some useful variations on that theme.  Just after I finished the series, Tal Galili, who maintains the R-bloggers website, pointed me to a variant I hadn’t seen before.  It's called a bee...

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Yeah Sure, Maybe, Well … Okay

March 23, 2011
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Yeah Sure, Maybe, Well … Okay

Whoever wrote the book on statistics, probably avoided getting a proper education in literature. At least that's my null hypothesis. The cryptic and awkward presentation of probabilities common amongst the Frequentists (no, not the Latin American Socia...

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Typos sorted, at last!

March 23, 2011
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Typos sorted, at last!

After posting so many entries about typos in my books (making you wonder how there could be any text left!) and postponing their classification for so long, I decided on Saturday afternoon to collect those entries into a comprehensive pdf document that should be more useful for readers. I incidentally noticed that my book web-page

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jStat: Advanced Statistics using Javascript

March 23, 2011
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jStat: Advanced Statistics using Javascript

While 'R' is getting enterprise ready, it's no longer the only open source option for advanced statistical programming. jStat.js is the new kid on the block.Things in favor of jStat:Based on Javascript, jQuery - future is assuredLight-weightAbility to ...

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basic ggplot2 network graphs – ver2

March 23, 2011
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basic ggplot2 network graphs – ver2

I posted last week a simple function to plot networks using ggplot2 package. Here is version 2. I still need to work on figuring out efficient vertex placement.Changes in version 2:-You have one of three options: use an igraph object, a matrix, or a da...

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The Popularity of Data Analysis Software (R vs SAS vs SPSS, etc.)

March 23, 2011
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The Popularity of Data Analysis Software (R vs SAS vs SPSS, etc.)

Robert Muenchen, the author of R for SAS and SPSS Users (A great book I’m proud to have on my shelf), has published this week an article in which he compares the popularity/market-share of many of the common statistical packages including R, SAS, SPSS and many others. The full article is available on r4stats.com at: “The Popularity of Data Analysis...

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