Blog Archives

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;DRThe software package has been...

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Self-written function help

Self-written function helpI 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 RI 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, 2014And 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 HooksIf 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 IncrementingA 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 / BioconductorWhat?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 MarkdownI 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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Hive Plots using R and Cytoscape

Hive Plots using R and Cytoscape

(This article was first published on Deciphering life: One bit at a time :: R, and kindly contributed to R-bloggers) I found out about HivePlots this past summer, and although I thought they looked incredibly useful and awesome, I didn't have a personal use for them at the time, and therefore put off doing anything with them. That recently...

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Storing package data in custom environments

Storing package data in custom environmentsIf you do R package development, sometimes you want to be able to store variables specific to your package, without cluttering up the users workspace. One way to do this is by modifying the global options. This is done by packages grDevices and parallel. Sometimes this doesn't seem to work quite right (see this...

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Tim Hortons Density

Tim Hortons Density

Tim Hortons DensityInspired by this post, I wanted to examine the locations and density of Tim Hortons restaurants in Canada. Using Stats Canada data, each census tract is queried on Foursquare for Tims locations.Setupoptions(stringsAsFactors = F) require(timmysDensity) require(plyr) require(maps) require(ggplot2) require(geosphere)Statistics Canada Census DataThe actual Statistics Canada data at the dissemination block level can be downloaded from here. You will want to...

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R Interface for Teaching

R Interface for TeachingKaitlin Thaney asked on Twitter last week about using Ramnath Vaidyanathan's new interactive R notebook 1 2 for teaching.Liking the look of interactive R notebook by @ramnath_vaidya. Any success stories in using to teach? http://t.co/wmVuFM2Rst (HT @_inundata)— Kaitlin Thaney (@kaythaney) July 9, 2013Now, to be clear up front,...

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