A few years ago I was involved in analysing some time-course microarray data. Our biological collaborators were interested in how we analysed their data, so this lead to a creation of tutorial, which in turn lead to a paper. When we submitted the paper, one the referees “suggested” that we write the paper using Sweave; 
I have become a complete knitr addict of late and have been using it in combination with RStudio’s R markdown support on a regular basis. In fact I wrote this post using it! It then dawned on me how great it would be if I … Continue reading →
When I am working in new institutions and I am asking: “Do you have a document management system?” I often get the answer:”Yap, we are using folders” … OKAY. Making analysis, developing applications and keeping an eye on code, data and applications make this even harder as it has to be. Of course not many
Note: this is a contributed article for the ICSA Bulletin and the basic idea can be summarized in this picture. It is hard to convince people to think about reproducible research (RR). There are two parts of difficulties: (1) tools used to be for ex...
I knew R was versatile, but DANG, people do a lot with it: > > … I don’t think anyone actually believes that R is designed to make *everyone* happy. For me, R does about 99% of the things I … Continue reading →
It’s gutted that I could not attend useR! 2012 after having a great time at useR!2011 at Warwick. However, a great active online community of useRs allows me to get lots of goods stuffs from the conference even though I did not attend physically. By keep following the #useR2012 and #rstats in Twitter and reading some great posts from R-bloggerRs on the 
Arguably, knitr (CRAN link) is the most outstanding R package of this year and its creator, Yihui Xie is the star of the useR! conference 2012. This is because the ease of use comparing to Sweave for making reproducible report. Integration of knitR and R Studio has made reproducible research much more convenience, intuitive and easier to 
GitHub is designed for collaborating on coding projects. Nonetheless, it is also a potentially great resource for researchers to make their data publicly available. Specifically you can use it to:store data in the cloud for future use (for free),track ...
R is hot and amazing. Tiki is too And with PluginR, we can easily place in simple or advanced web reports any R code, in a similar fashin to what can be achieved with other longer combinations (Sweave, Knitr, ... and latex).
For instance, I tried a few days ago to quickly...
The following post documents the steps I needed to take in order to convert a project using Sweave LaTeX into one using knitr LaTeX. Additional Resources It is fairly straightforward to convert a document from Sweave LaTeX to knitr LaTeX. Yihui Xie on...
Zero Inflated Models and Generalized Linear Mixed Models with R.
Zuur, Saveliev, Ieno (2012).
