A Fast Intro to PLYR for R

August 27, 2009
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A Fast Intro to PLYR for R

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

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Using R and Bioconductor for sequence analysis

August 26, 2009
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Using R and Bioconductor for sequence analysis

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...

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

August 25, 2009
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ggplot2 Version of Figures in “Lattice: Multivariate Data Visualization with R” (Final Part)

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

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Web-site trend analysis with data from Google Analytics

August 25, 2009
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Web-site trend analysis with data from Google Analytics

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...

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Web-site trend analysis with data from Google Analytics

August 25, 2009
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Web-site trend analysis with data from Google Analytics

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...

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Applied Spatial Data Analysis with R

August 25, 2009
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Applied Spatial Data Analysis with R

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

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Standardized Velvet Assembly Report

August 25, 2009
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Standardized Velvet Assembly Report

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...

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Standardized Velvet Assembly Report

August 25, 2009
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Standardized Velvet Assembly Report

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...

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packages and CRANtastic

August 24, 2009
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packages and CRANtastic

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...

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CO2 Emission Trends

August 23, 2009
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CO2 Emission Trends

“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

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R help on StackOverflow

August 23, 2009
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R help on StackOverflow

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.

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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 goo...

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R handy for crunching data

August 23, 2009
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R handy for crunching data

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

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NpptoR: R in Notepad++

August 22, 2009
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NpptoR: R in Notepad++

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

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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 ...

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No success yet, then more animations…

August 20, 2009
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No success yet, then more animations…

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...

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No success yet, then more animations…

August 20, 2009
By
No success yet, then more animations…

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...

Read more »

Simple logistic regression on qualitative dichotomic variables

August 20, 2009
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Simple logistic regression on qualitative dichotomic variables

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...

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Simple logistic regression on qualitative dichotomic variables

August 20, 2009
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Simple logistic regression on qualitative dichotomic variables

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...

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

August 20, 2009
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ggplot2 Version of Figures in “Lattice: Multivariate Data Visualization with R” (Part 13)

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

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2 Interesting animations…

August 19, 2009
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2 Interesting animations…

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...

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2 Interesting animations…

August 19, 2009
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2 Interesting animations…

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...

Read more »

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...

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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 and other...

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

August 18, 2009
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ggplot2 Version of Figures in “Lattice: Multivariate Data Visualization with R” (Part 12)

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

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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.

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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.

Read more »

The density function

August 18, 2009
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The density function

Today I found such an interesting function called "density", this function computes kernel density estimates, that's why I found it pretty interesting, all you need is:the the data from which the estimate is to be computed the smoothing kernel to be us...

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The density function

August 18, 2009
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The density function

Today I found such an interesting function called "density", this function computes kernel density estimates, that's why I found it pretty interesting, all you need is:the the data from which the estimate is to be computed the smoothing kernel to be us...

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