Travis-CI to Github Pages I don't remember how I got on this, but I believe I had a recent twitter exchange with some persons (or saw it fly by) about pushing R package vignettes to the web after building and checking on travis-ci. Hadley Wickham pointed to using such a ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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. ... [Read more...]

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 ... [Read more...]

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 ... [Read more...]

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, ... [Read more...]

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 ... [Read more...]

Storing package data in custom environments If 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. ... [Read more...]

Tim Hortons Density Inspired 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. Setup

options(stringsAsFactors = F)
require(timmysDensity)
require(plyr)
require(maps)
require(ggplot2)
require(geosphere)

Statistics Canada Census Data The actual Statistics Canada data at the dissemination block ... [Read more...]

R Interface for Teaching Kaitlin 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, 2013 Now, ... [Read more...]

Using Samatha So I decided to try out David Springates Samatha package for statically building this blog. If you decide to use it, be warned, right now it is a little rough around the edges, and needs some work. David created his own blog using it, and has been using ... [Read more...]

Pre-calculating large tables of values I'm currently working on a project where we want to know, based on a euclidian distance measure, what is the probability that the value is a match to the another value. i.e. given an actual value, and a theoretical value from calculation, what is ... [Read more...]

Open VS Closed Analysis Languages TL;DR I think data scientists should choose to learn open languages such as R and python because they are open in the sense that anyone can obtain them, use them and modify them for free, and this has lead to large, robust groups of ... [Read more...]

R, RStudio, and release and dev Bioconductor I have one Bioconductor package that I am currently responsible for. Each bi-annual release of Bioconductor requires testing and squashing errors, warnings and bugs in a given package. Doing this means being able to work with multiple versions of R and multiple versions ... [Read more...]

Portable, personal packages ProgrammingR had an interesting post recently about keeping a set of R functions that are used often as a gist on Github, and sourceing that file at the beginning of R analysis scripts. There is nothing inherently wrong with this, but it does end up cluttering the ... [Read more...]