Blog Archives

Packages vs ProjectTemplate

Packages vs ProjectTemplate tl;dr Imposing a different structure than R packages for distributing R code is a bad idea, especially now that R package tools have gotten to the point where managing a package has become much easier. ProjectTemplate ?? My last two posts (1, 2) provided an argument and an example of why one should use R packages to contain...

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Creating an analysis as a package and vignette

Creating an analysis as a package and vignette Following from my last post, I am going to go step by step through the process I use to generate an analysis as a package vignette. This will be an analysis of the tweets from the 2012 and 2014 ISMB conference (thanks to Neil and Stephen for...

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Analyses as Packages

Analyses as Packages TL;DR Instead of writing an analysis as a single or set of R scripts, use a package and include the analysis as a vignette of the package. Read below for the why, the how is in the next post. Analyses and Reports As data science or statistical researchers, we tend to do a lot of analyses, whether for our...

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R Job Notifications Using Twitter

R Job Notifications Using Twitter There has been some interesting activity about getting R to send a notification somehow when a long running job is completed. The most notable entries I have seen in this category are RPushBullet for web notifications and pingr for audio notifications. Although RPushBullet looks really cool (and Dirk does great work), I wondered...

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categoryCompare Paper Finally Out!

categoryCompare Paper Finally Out! I can finally say that the publication on my Bioconductor package categoryCompare is finally published in the Bioinformatics and Computational Biology section of Frontiers in Genetics. This has been a long time coming, and I wanted to give some background on the inspiration and development of the method and software. TL;DR The software package has been...

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Self-written function help

Self-written function help I have noted at least one instance (and there are probably others) about how Python's docStrings are so great, and wouldn't it be nice to have a similar system in R. Especially when you can have your new function tab completion available depending on your development environment. This is a false statement, however. If you set...

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Installing MatLab vs Installing R

Installing MatLab vs Installing R I retweeted this a few days ago: 1. Open MATLAB for first time in a few years after using #rstats. 2. Site license doesn't work right. 3. F*** MATLAB, I'll try to do it in R— Andrew D. Steen (@drdrewsteen) February 6, 2014 And as I have started the process of installing MatLab on my...

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Package Version Increment Pre- and Post-commit Hooks

Package Version Increment Pre- and Post-commit Hooks If you just want the hook scripts, check this gist. If you want to know some of the motivation behind writing them, and about the internals, then read on. Package Version Incrementing A good practice to get into is incrementing the minor version number (i.e. going from 0.0.1 to 0.0.2) after each git commit...

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Creating custom CDF for Affy chips in R / Bioconductor

Creating custom CDF for Affy chips in R / Bioconductor What? For those who don't know, CDF files are chip definition format files that define which probes belong to which probesets, and are necessary to use any of the standard summarization methods such as RMA, and others. Why? Because we can, and because custom definitions have been shown to be quite useful. See...

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Writing papers using R Markdown

Writing papers using R Markdown

Writing papers using R Markdown I have been watching the activity in RStudio and knitr for a while, and have even been using Rmd (R markdown) files in my own work as a way to easily provide commentary on an actual dataset analysis. Yihui has proposed writing papers in markdown and posting them to a blog as a way...

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