New RInside release

July 19, 2009
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I just rolled up a new release of RInside, my C++ wrapper classes which facilitate embedding R into your own C++ application. This releases owes a big Thank you! to Miguel Lechón who not only noticed errant behaviour and occassional segfaults with ov...

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New RInside release

July 19, 2009
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I just rolled up a new release of RInside, my C++ wrapper classes which facilitate embedding R into your own C++ application. This releases owes a big Thank you! to Miguel Lechón who not only noticed errant behaviour and occassional segfaults with overly long commands sent to the embedded R, but even traced it to an oversight of mine in a simple memory buffer class...

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David Varadi’s RSI(2) alternative

July 19, 2009
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David Varadi’s RSI(2) alternative

Here's a quick R implementation of David Varadi's alternative to the RSI(2).  Michael Stokes over at the MarketSci blog has three great posts exploring this indicator: Varadi’s RSI(2) Alternative: The DV(2) RSI(2) vs. DV(2) Last Couple...

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A probability exercise on the Bernoulli distribution

July 18, 2009
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A probability exercise on the Bernoulli distribution

What is the probability, flipping a coin 8 times, to obtain the sequence HHTTTHTT? (H = head; T= tail)The theory teaches us that to solve this question, we can simply use the following formula:$$f(x)=P(X=x)=B(n,p)=\begin{pmatrix}n\\ x \end{pmatrix} \cd...

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Let us practice with some functions of R

July 18, 2009
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Let us practice with some functions of R

Given the following data set, compute the arithmetic mean, median, variance, standard deviation; find the greatest and the smaller value, the sum of all values, the square of the sum of all values, the sum of the square of all values; assigne the ranks...

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Book excerpts now posted

July 18, 2009
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Book excerpts now posted

We've posted excerpts from the book on the book website. The excerpts include Chapter 3 (regression and ANOVA) in its entirety. This demonstrates how the entries (the generic descriptions of software functions) and the worked examples reinforce each ...

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Parsing GEO SOFT files with Python and Sqlite

July 17, 2009
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Parsing GEO SOFT files with Python and Sqlite

NCBI's GEO database of gene expression data is a great resource, but its records are very open ended. This lack of rigidity was perhaps necessary to accommodate the variety of measurement technologies, but makes getting data out a little tricky. But, a...

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Simple Data Visualization

July 16, 2009
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Simple Data Visualization

OK, so, I know I already raved about one Hadley Wickham project and how it has changed my life last week. But what can I say, the man is a genius. And if you are using R (and let’s face it, you should be) and you want simple sexy graphs made quick, the man has

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Influence.ME: Simple Analysis

July 16, 2009
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Influence.ME: Simple Analysis

With the introduction of our new package for influential data influence.ME, I’m currently writing a manual for the package. This manual will address topics for both the experienced, and the inexperienced users. I will also present much of the content ...

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Missing data, logistic regression, and a predicted values plot (or two)

July 15, 2009
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miss attach miss result1 summary(result1) Call: glm(formula = a ~ b, family = binomial(logit)) Deviance Residuals: Min 1Q Median 3Q Max -1.8864 -1.2036 0.7397 0.9425 1.4385 Coefficients: ...

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Missing data, logistic regression, and a predicted values plot (or two)

July 15, 2009
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miss attach miss result1 summary(result1) Call: glm(formula = a ~ b, family = binomial(logit)) Deviance Residuals: Min 1Q Median 3Q Max -1.8864 -1.2036 0.7397 0.9425 1.4385 Coefficients: ...

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Job grade plot

July 15, 2009
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Job grade plot

This plot:was created using the following R code:plot (q9e~q8, type = "n",xlim = c(1,13), ylim = c(1,13),cex.lab=1.25,cex.axis=0.75, col.lab = "#333333", xlab = "Obama job grade",ylab = "Congressional job grade", xaxt ="n", yaxt="n",main="Obama and Co...

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Job grade plot

July 15, 2009
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Job grade plot

This plot:was created using the following R code:plot (q9e~q8, type = "n",xlim = c(1,13), ylim = c(1,13),cex.lab=1.25,cex.axis=0.75, col.lab = "#333333", xlab = "Obama job grade",ylab = "Congressional job grade", xaxt ="n", yaxt="n",main="Obama and Co...

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Example 7.5: Replicating a prettier jittered scatterplot

July 15, 2009
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Example 7.5: Replicating a prettier jittered scatterplot

The scatterplot in section 7.4 is a plot we could use repeatedly. We demonstrate how to create a macro (SAS, section A.8) and a function (R, section B.5) to do it more easily.SAS%macro logiplot(x=x, y=y, data=, jitterwidth=.05, smooth=50);data lp1;set...

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Building R packages for Windows

July 13, 2009
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Building R packages for Windows

1. Installing the required tools To build an R package in Windows, you will need to install some additional software tools. These are summarized at http://www.murdoch-sutherland.com/Rtools 1.1 Essential: Rtools This is a collection of unix-like tools that can be run from the DOS command prompt. It also contains the MinGW compilers that are used for

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Building R packages for Windows

July 13, 2009
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1. Installing the required tools To build an R package in Windows, you will need to install some additional software tools. These are summarized at http://www.murdoch-sutherland.com/Rtools 1.1 Essential: Rtools This is a collection of unix-like tools...

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A recommended book

July 13, 2009
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A recommended book

I've been getting a lot of help from this book:While written for S-Plus, nearly everything in it is applicable with R.

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A recommended book

July 13, 2009
By
A recommended book

I've been getting a lot of help from this book:While written for S-Plus, nearly everything in it is applicable with R.

Read more »

cran2deb: Would you like 1700+ new Debian / R packages ?

July 13, 2009
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As I mentioned in my quick write-up of UseR 2009, one of my talks was about cran2deb: a system to turn (essentially) all CRAN packages into directly apt-get-able binary packages. This is essentially a '2.0' version of earlier work with Steffen Moel...

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cran2deb: Would you like 1700+ new Debian / R packages ?

July 13, 2009
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As I mentioned in my quick write-up of UseR 2009, one of my talks was about cran2deb: a system to turn (essentially) all CRAN packages into directly apt-get-able binary packages. This is essentially a '2.0' version of earlier work with Steffen Moelle...

Read more »

cran2deb: Would you like 1700+ new Debian / R packages ?

July 13, 2009
By

As I mentioned in my quick write-up of UseR 2009, one of my talks was about cran2deb: a system to turn (essentially) all CRAN packages into directly apt-get-able binary packages. This is essentially a '2.0' version of earlier work with Steffen Moel...

Read more »

Some detail on the last plot

July 13, 2009
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Some detail on the last plot

First we plot approval (app) against date (daten). We also specify a few other things. ylim=c(40,80) specifies that the y axis extends from 40 to 80. xlim=c(-3,210) might seem odd, but we need extra space on the left. pch=16 plots dots, and col="gray" ...

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Some detail on the last plot

July 13, 2009
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Some detail on the last plot

First we plot approval (app) against date (daten). We also specify a few other things. ylim=c(40,80) specifies that the y axis extends from 40 to 80. xlim=c(-3,210) might seem odd, but we need extra space on the left. pch=16 plots dots, and col="gray" ...

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Obama approval

July 12, 2009
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Obama approval

Working some more with time series data. Here we have a graph of Obama job approval numbers, with two LOWESS-fit lines added for trending:Figure1. President Obama job approval, Jan 2009 - present.There's actually some pretty fancy stuff going on there, as the following code shows.polls lfit1 lfit2 plot (app~daten, ylim=c(40,80), xlim=c(-3,210),pch=16, col="gray",cex.lab=1.25,cex.axis=0.75,col.lab = "#777777", xlab="",ylab="Obama...

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Obama approval

July 12, 2009
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Obama approval

Working some more with time series data. Here we have a graph of Obama job approval numbers, with two LOWESS-fit lines added for trending: Figure1. President Obama job approval, Jan 2009 - present.There's actually some pretty fancy stuff going on there, as the following code shows.polls lfit1 lfit2 plot (app~daten, ylim=c(40,80), xlim=c(-3,210),pch=16, col="gray",cex.lab=1.25,cex.axis=0.75,col.lab = "#777777", xlab="",ylab="Obama...

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useR 2009 in Rennes: Recap and slides

July 12, 2009
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I spent most of last week in Rennes, the capital of Brittany in France, as it was time for UseR! 2009, the annual R conference. Francois Husson, Aline Legrand and others at the Agrocampus Ouest had put together a really well-run conference, and it w...

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useR 2009 in Rennes: Recap and slides

July 12, 2009
By

I spent most of last week in Rennes, the capital of Brittany in France, as it was time for UseR! 2009, the annual R conference. Francois Husson, Aline Legrand and others at the Agrocampus Ouest had put together a really well-run conference, and it was ...

Read more »

useR 2009 in Rennes: Recap and slides

July 12, 2009
By

I spent most of last week in Rennes, the capital of Brittany in France, as it was time for UseR! 2009, the annual R conference. Francois Husson, Aline Legrand and others at the Agrocampus Ouest had put together a really well-run conference, and it w...

Read more »

Causal inference and biostatistics

July 11, 2009
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I've been following the discussion on causal inference over at Gelman's blog with quite a bit of interest. Of course, this is in response to Judea Pearl's latest book on causal inference, which differs quite a bit from the theory that had been forwarde...

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