Blog Archives

A Few Notes on UseR! 2014

July 25, 2014
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A Few Notes on UseR! 2014

It has been a month since the UseR! 2014 conference, and I'm probably the last one who writes about it. UseR! is my favorite conference because it is technical and not too big. I have completely lost interest in big and broad conferences like JSM (to me, it has become Joint Sightseeing Meetings). Karl has written two blog posts...

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library() vs require() in R

July 25, 2014
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library() vs require() in R

While I was sitting in a conference room at UseR! 2014, I started counting the number of times that require() was used in the presentations, and would rant about it after I counted to ten. With drums rolling, David won this little award (sorry, I did not really mean this to you). Ladies and gentlemen, I've said this before:...

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R Markdown v2

June 18, 2014
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R Markdown v2

People rarely agree on a best authoring tool or language. Some people cannot live without \LaTeX{} because of the beauty and quality of its PDF output. Some \feel{} \uncomfortable{} \with{} \backslashes{}, and would rather live in another World Word. We have also witnessed the popularity of Markdown, an incredibly simple language (seriously? a LANGUAGE?) that has made reproducible research much easier.

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Markdown or LaTeX?

October 19, 2013
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Markdown or LaTeX?

What happens if you ask for too much power from Markdown? R Markdown is one of the document formats that knitr supports, and it is probably the most popular one. I have been asked many times about the choice between Markdown and LaTeX, so I think I'...

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Testing R Packages

September 29, 2013
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This guy th3james claimed Testing Code Is Simple, and I agree. In the R world, this is not anything new. As far as I can see, there are three schools of R users with different testing techniques: tests are put under package/tests/, and a foo-test.Rout.save from R CMD BATCH foo-test.R; testing is done by comparing foo-test.Rout from R CMD check with your foo-test.Rout.save; R...

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After Three Months I Cannot Reproduce My Own Book

September 5, 2013
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After Three Months I Cannot Reproduce My Own Book

I thought I could easily jump to a high standard (reproducibility), but I failed. Some of you may have noticed that the knitr book is finally out. Amazon is offering a good price at the moment, so if you are interested, you'd better hurry up. I a...

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My first Bioconductor conference (2013)

July 21, 2013
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My first Bioconductor conference (2013)

The BioC 2013 conference was held from July 17 to 19. I attended this conference for my first time, mainly because I'm working at the Fred Hutchinson Cancer Research Center this summer, and the conference venue was just downstairs! No flights, no hotel...

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R Package Versioning

June 27, 2013
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R Package Versioning

This should be what it feels like to bump the major version of your software: For me, the main reason for package versioning is to indicate the (slight or significant) differences among different versions of the same package, otherwise we can keep o...

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You Do Not Need to Tell Me I Have A Typo in My Documentation

June 10, 2013
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You Do Not Need to Tell Me I Have A Typo in My Documentation

So I just got yet yet another comment saying "you have a typo in your documentation". While I do appreciate these kind reminders, I think it might be a good exercise for those who want to try GIT and Github pull requests, which make it possible for y...

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A Few Tips for Writing an R Book

June 3, 2013
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A Few Tips for Writing an R Book

I just finished fixing (hopefully all) the problems in the knitr book returned from the copy editor. David Smith has kindly announced this book before I do. I do not have much to say about this book: almost everything in the book can be found in the on...

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