## Learning R 2009-08-28 13:11:00

August 28, 2009
By

fydeficit.1projectedpng("c:/data/deficit_color.png",height=480,width=480)plot(deficit.1~fy,ylim=c(-12,5),type="n",lwd=2,col="red",main="Federal budget deficit, 1990-2019",cex.lab=1.1,cex.axis=.75,xlab="Fiscal year",ylab="Deficit (% of GDP)")rect(1988,-15,1994,6,col="#FF9999",border=NA)rect(1994,-15,2002,6,col="#6699FF",border=NA)rect(2002,-15,2010,6,col="#FF9999",border=NA)rect(2010,-15,2014,6,col="#6699FF",border=NA)rect(2014,-15,2021,6,col="#CCCCCC",border=NA)abline(h=0,lwd=.5,lty=3,col="#555555")lines(fy,deficit.1,lwd=2.5)lines(fy,projected,lwd=2.5,lty=2)rect(1990,-11.5,2000,-9.5,col="#dddddd",border="#555555")text(1995,-10.5,"Source: CBO")graphics.off()

## Combine R CMD build and junit

August 28, 2009
By

This is a post in the series Mixing R CMD build and ant. Previous posts have shown how to compile the java code that lives in the src directory of a package and how to document this code using javadoc. This post tackles the problem of unit testin...

## A Fast Intro to PLYR for R

August 27, 2009
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I’m not dead yet! Although it has been rumored that I am. The new job is going great and I’m thrilled to be with a new firm doing interesting work alongside smart people. It makes me seem smarter by simple association. There’s been a lot going on recently in the R user community. There was an

## Using R and Bioconductor for sequence analysis

August 26, 2009
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Here's another quick R vignette, in case I pick this up later and need to remind myself where I got stuck. I was trying to use R for a bit of basic sequence analysis, with mixed results.First, install the BSgenome package, which is part of Bioconductor...

## ggplot2 Version of Figures in “Lattice: Multivariate Data Visualization with R” (Final Part)

August 25, 2009
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Over the past weeks I have tried to replicate the figures in Lattice: Multivariate Data Visualization with R using Hadley Wickham’s ggplot2. With the exception of a few graph types (e.g. ggplot2 doesn’t support 3d-graphs, and there were a few other cases), it was possible to create ggplot2 versions of almost all the figures. Sometimes this

## Web-site trend analysis with data from Google Analytics

August 25, 2009
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This post is a summary of my two previous posts on the trend analysis with the Cox-Stuart test and on simple linear regression. The goal that we propose is to assess the trend in the number of visits received from a site over a long time. I use Google Analytics, because this tool allows us to save...

## Web-site trend analysis with data from Google Analytics

August 25, 2009
By

This post is a summary of my two previous posts on the trend analysis with the Cox-Stuart test and on simple linear regression. The goal that we propose is to assess the trend in the number of visits received from a site over a long time. I use Google Analytics, because this tool allows us to save...

## Applied Spatial Data Analysis with R

August 25, 2009
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I have just reviewed the book Applied Spatial Data Analysis with R which has been published in the September2009  issue of the Royal Statistical Society’s Significance magazine. Applied Spatial Data Analysis with R is an accessible text that demonstrates and explains the handling of spatial data using the R Software Platform. The text’s authors have

## Standardized Velvet Assembly Report

August 25, 2009
By

http://code.google.com/p/standardized-velvet-assembly-report/I finally got my Velvet Assembler report script up on google code. This "program" consists of some short scripts and a Sweave report designed to help Velvet users identify the optimal kmer an...

## Standardized Velvet Assembly Report

August 25, 2009
By

http://code.google.com/p/standardized-velvet-assembly-report/I finally got my Velvet Assembler report script up on google code. This "program" consists of some short scripts and a Sweave report designed to help Velvet users identify the optimal kmer an...

## packages and CRANtastic

August 24, 2009
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Additional functionality in R is added through packages, which consist of libraries of bundled functions, datasets, examples and help files that can be downloaded from CRAN (the Comprehensive R Archive Network). The function install.packages() or the w...

## CO2 Emission Trends

August 23, 2009
By

“Since 1751 approximately 329 billion tons of carbon have been released to the atmosphere from the consumption of fossil fuels and cement production. Half of these emissions have occurred since the mid 1970s. The 2006 global fossil-fuel carbon emission estimate, 8230 million metric tons of carbon, represents an all-time high and a 3.2% increase

## R help on StackOverflow

August 23, 2009
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Ever since I began using R about ten years ago, the best place to find R help was on the R-help mailing list. But it is time-consuming searching through the archives trying to find something from a long time ago, and there is no way to sort out the good advice from the bad advice.

## R help on StackOverflow

August 23, 2009
By

Ever since I began using R about ten years ago, the best place to find R help was on the R-help mailing list. But it is time-consuming searching through the archives trying to find something from a long time ago, and there is no way to sort out the goo...

## R handy for crunching data

August 23, 2009
By

http://www.ibm.com/developerworks/library/l-sc16.html?S_TACT=105AGX52&S_CMP=cn-a-l

August 22, 2009
By

For those who are scared of Emacs: http://sourceforge.net/projects/npptor/

## Test cointegration with R

Cointegrated pairs of securities are crucial for mean reversion trading portfolio construction, Play with cointegration has several good papers to start with. Should you want to test pairs of securities for cointegration using R, here is an excellent ...

## No success yet, then more animations…

August 20, 2009
By

So I've been here dealing with the installation of a software that Yihui Xie suggested me to change the format of the animations displayed in R, she told me that all I needed to do was to go to http://imagemagick.org to download ImageMagick for my ope...

## No success yet, then more animations…

August 20, 2009
By

So I've been here dealing with the installation of a software that Yihui Xie suggested me to change the format of the animations displayed in R, she told me that all I needed to do was to go to http://imagemagick.org to download ImageMagick for my ope...

## Simple logistic regression on qualitative dichotomic variables

August 20, 2009
By

In this post we will see briefly how to implement a logistic regression model if you have categorical variables, or qualitative, organized in double entry contingency tables. In this model the dependent variable (Y) and independent variable (X) are both dichotomies (or Bernoullian).In general, the probability that Y = 1 as a function of predictors is:$$P(Y=1|X=x)=\pi(x)=\frac{exp(\beta_0+\beta_1x_1+\cdots +\beta_kx_k)}{1+exp(\beta_0+\beta_1x_1+\cdots +\beta_kx_k)}$$Our goal...

## Simple logistic regression on qualitative dichotomic variables

August 20, 2009
By

In this post we will see briefly how to implement a logistic regression model if you have categorical variables, or qualitative, organized in double entry contingency tables. In this model the dependent variable (Y) and independent variable (X) are both dichotomies (or Bernoullian).In general, the probability that Y = 1 as a function of predictors is:$$P(Y=1|X=x)=\pi(x)=\frac{exp(\beta_0+\beta_1x_1+\cdots +\beta_kx_k)}{1+exp(\beta_0+\beta_1x_1+\cdots +\beta_kx_k)}$$Our goal...

## ggplot2 Version of Figures in “Lattice: Multivariate Data Visualization with R” (Part 13)

August 20, 2009
By

This is the 13th post in a series attempting to recreate the figures in Lattice: Multivariate Data Visualization with R (R code available here) with ggplot2. Previous parts in this series: Part 1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7, Part 8, Part 9, Part 10, Part 11, Part 12. Chapter 14

## 2 Interesting animations…

August 19, 2009
By

So I haven't had success YET in finding a way to post here the animations, but I thought it would be interesting to show you at least a couple of examples using this software, and I chose 2 pretty interesting ones by Yihui Xie and Xiaoyue Cheng.The fir...

## 2 Interesting animations…

August 19, 2009
By

So I haven't had success YET in finding a way to post here the animations, but I thought it would be interesting to show you at least a couple of examples using this software, and I chose 2 pretty interesting ones by Yihui Xie and Xiaoyue Cheng.The fir...

## Have you ever heard about the ‘animation package’?

August 18, 2009
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Well, I had never heard about it, but this morning I was looking for some information about another package and I found and article about this interesting package at 'The R-Journal' (http://journal.r-project.org/), it was on the Vol. 8/2, October 2008, by Yihui Xie and Xiaoyue Cheng, and it says something like..."The animation package (Xie, 2008) uses graphical andother...

## Have you ever heard about the ‘animation package’?

August 18, 2009
By

Well, I had never heard about it, but this morning I was looking for some information about another package and I found and article about this interesting package at 'The R-Journal' (http://journal.r-project.org/), it was on the Vol. 8/2, October 2008, by Yihui Xie and Xiaoyue Cheng, and it says something like... "The animation package (Xie, 2008) uses graphical and other...

## ggplot2 Version of Figures in “Lattice: Multivariate Data Visualization with R” (Part 12)

August 18, 2009
By

This is the 12th post in a series attempting to recreate the figures in Lattice: Multivariate Data Visualization with R (R code available here) with ggplot2. Previous parts in this series: Part 1, Part 2, Part 3, Part 4, Part 5, Part 6, Part 7, Part 8, Part 9, Part 10, Part 11. Chapter 13 – Advanced

## R Coding Style Guide

August 18, 2009
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I was sent this R style guide, and think it looks like it might be a good idea. R can be pretty difficult to read, especially someone else's.