A while ago, a friend of mine needed to download a number of different DNA sequences from Genbank, the online repository for the vast majority of DNA sequences read from all organisms by labs all over the world. This is not a problem. The "ape" package in R has a nifty function, read.GenBank(), that downloads the...
Downloading DNA sequences into R
A while ago, a friend of mine needed to download a number of different DNA sequences from Genbank, the online repository for the vast majority of DNA sequences read from all organisms by labs all over the world. This is not a problem. The "ape" package in R has a nifty function, read.GenBank(), that downloads the...
Two Surpising Things about R
I see that it’s been over a year since my last post! I have a backlog of blog post ideas, but something else always seems to have higher priority. Today, though, I have some interesting (and useful) things to say about R, which I discovered in the last few days, and which shouldn’t take long 
Hard drive occupation prediction with R – The linear regression
On some environments, disk space usage can be pretty predictable. In this post, we will see how to do a linear regression to estimate when free space will reach zero, and how to assess the quality of such regression, all using R - the statistical soft...
Hard drive occupation prediction with R
On some environments, disk space usage can be pretty predictable. In this post, we will see how to do a linear regression to estimate when free space will reach zero, and how to assess the quality of such regression, all using R - the statistical soft...
Auto-completion in Notepad++ for R Script
Auto-completion is fancy in a text editor. Notepad++ does not support auto-completion for the R language, so I spent a couple of hours on creating such an XML file to support R: Put it under ‘plugins/APIs‘ in the installation directory of Notepad++ (you can see several other XML files there supporting different languages such as
Introducing visualVaR.com
After a month of on-again, off-again coding, I’ve finally completed a web site geared towards calculating the Value at Risk of the average investor’s portfolio. The site is visualvar.com. The big idea was to combine the statistical and visualization tools of R (especially ggplot2) with the web interface of Drupal. While I’m
Presentations and video from useR! 2010 available
For anyone who missed the useR! 2010 conference in Gaithersburg last month (or just wants to revisit some of the amazing talks), you can now find slides from many of the contributed presentations available for download. (Look for the link to download slides.) The presentations from the Revolution team members are there, including: My presentation on Evolving R...
Apologies and Style Guides
I have to say that it’s pretty exciting to watch your blog go from a few hits over its lifetime to getting almost 200 in a single day. I am currently negotiating with Google over the purchase of this blog. Or maybe not. Again, thanks be to @revodavid for posting to the Revolution Analytics Blog. 
Rcpp svn revision 2000
I commited the 2000th revision of Rcpp svn today, so I wanted to look back at what I did previously with the 50 000th R commit.
Here are the number of commits per day and month
Read more »Scrape Web data using R
Plenty of people have been scraping data from the web using R for a while now, but I just completed my first project and I wanted to share the code with you. It was a little hard to work through some of the “issues”, but I had some great help from @DataJunkie on twitter. As 
Rcpp at LondonR, oct 5th
I'll be presenting Rcpp at the next LondonR, which is currently scheduled for october 5th Here is one picture I found on flickr, searching for london speed bus, ... there are many other
Fun with the proto package: building an MCMC sampler for Bayesian regression
The proto package is my latest favourite R goodie. It brings prototype-based programming to the R language - a style of programming that lets you do many of the things you can do with classes, but with a lot less up-front work. Louis Kates and Thomas Petzoldt provide an excellent introduction to using proto in the
Fun with the proto package: building an MCMC sampler for Bayesian regression
The proto package is my latest favourite R goodie. It brings prototype-based programming to the R language - a style of programming that lets you do many of the things you can do with classes, but with a lot less up-front work. Louis Kates and Thomas P...
Tuning Notepad++
Here are some tricks I collected for making Notepad++ a more comfortable text editor for me in general in for the R programming language in particular.Switch between tabs in Notepad++ with Ctrl-PageUp/DownNotepad++'s default behaviour is to use Ctrl+(S...
R’s role in the national response to the BP Oil Spill
In the early days of the Deepwater Horizon oil spill in the Gulf of Mexico, the rate of flow of oil from the spill was of great concern: estimating it accurately was key to coordinating the scale and scope of the response to the emergency. Unfortunately, estimates from independent sources varied widely, and BP's own estimates varied widely over...
useR! 2010 conference videos
Videos of the invited talks of the useR! 2010 conference as follows (courtesy by Kate Mullen and NIST). This site also aims at collecting the materials (video, slides, R code) of local R users group (RUG) meetings and various other … Continue reading →
Baseball games: getting longer?
ESPN's Bill Simmons (aka The Sports Guy) recently suggested that the primary cause of dwindling interest in Red Sox games by fans is that baseball games these days are too long. "It's not that fun to spend 30-45 minutes driving to a game, paying for parking, parking, waiting in line to get in, finding your seat ... and then,...
What would a 25th, 50th, and 75th percentile soil profile look like?
I have mentioned the AQP package in previous entries. One of the functions in this package generates aggregate soil profile data, from a collection of soil profiles that are related by some factor: common lithology, common landscape position, and so on...
Using R for Introductory Statistics 3.3
...continuing our way though John Verzani's Using R for introductory statistics. Previous installments: chapt1&2, chapt3.1, chapt3.2 Relationships in numeric data If two data series have a natural pairing (x1,y1),...,(xn,yn), then we can ask, &ld...
Using R for Introductory Statistics 3.3
...continuing our way though John Verzani's Using R for introductory statistics. Previous installments: chapt1&2, chapt3.1, chapt3.2 Relationships in numeric data If two data series have a natural pairing (x1,y1),...,(xn,yn), then we can ask, &ld...
Converting R contingency tables to data frames
A contingency table presents the joint density of one or more categorical variables. Each entry in a contingency table is a count of the number of times a particular set of factors levels occurs in the dataset. For example, consider a list of plant ...
Converting R contingency tables to data frames
A contingency table presents the joint density of one or more categorical variables. Each entry in a contingency table is a count of the number of times a particular set of factors levels occurs in the dataset. For example, consider a list of plant ...
Which chart is better?
CHART CRITICS, GRAPHICS CURMUDGEONS, COME ONE COME ALL Once upon a time there was this graph (graph 1). Andrew Gelman went all graphics curmudgeon on it, calling it an “ugly, sloppy bit of data graphics“, so it became this graph (graph 2). Now the question is, which is better: graph 2 or graph 3? Please
R Environments for Gibbs Sampler State
I recently decided to revisit some R code that implements a Gibbs sampler in an attempt to decrease the iteration time. My strategy was to implement the sampler state as an R environment rather than a list. The rationale was that passing an environment to and from functions would reduce the amount of duplication (memory
Conditioning Systems on Regime Variables
Here is a brief and simple example of switching systems based upon regime type (sometimes called gating). I've brought up the idea of conditioning systems based upon regimes many times in past posts. Some texts call this filtering, although I prefer t...
A Twitter feed for R links
India-based data scientist Harsh Singhal has compiled "State of the R": a list of more than 50 links to R-related websites, which has generated much discussion on the R Project group on LinkedIn. Now, even if you're not on LinkedIn, you can find the list at the new Links4R Twitter profile, and get updates about new links by following...
Just for Fun: Using R to Create Targets
OK, not really science or soil-related, but a fun 5 minute use of R to make something you can use to improve your hand-eye coordination. read more
Homogeneity analysis of hierarchical classifications
I've spent more years than I care to remember analysing vegetation survey data (typically species abundances in plots) using a variety of software including my own algorithms coded in FORTRAN and C++. A recent query on the r-help list, about how to determine the number of groups to define in a hierarchical classification produced with the hclust function, prompted...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
