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...
In case you missed it: November 2013 Roundup
In case you missed them, here are some articles from October of particular interest to R users: A recap of the Strata Hadoop World conference, including presentations from Monsanto...
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...
RcppArmadillo 0.3.930.1
A new Armadillo release 3.930 came out a few days ago, with a very nice set of changes (see below). I rolled this into RcppArmadillo 0.3.930.0. However, one of...
Next Kölner R User Meeting: 13 December 2013
Quick reminder: The next Cologne R user group meeting is scheduled for this Friday, 13 December 2013. We are delighted to welcome:
Matt Dowle and Arun Srinivasan: Introduction to
eeptools 0.3 Released!
Version 0.3 of my R package of miscellaneous code has been released, this time with substantial contributions from Jason Becker via GitHub. Progress continues toward the ultimate goal for eeptools to...
24 Days of R: Day 9
This will be the third time I've tried to write this post. I had started out presuming that I would uncover something fascinating about applying Bayesian inference to a...
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...
Matrix factorizations and social network graph analysis
This is a lecture post for my students in the CUNY MS Data Analytics program. In this series of lectures …Continue reading »
The Tornado Project
GoalBring consistency and transparency to the analyses of publicly available Tornado datasets using an R-based open source analysis.IssuesTornado data available from the NOAA Storm Prediction Center and other government agencies...
Intentionally Writing Obtuse Code
Sometimes intentionally writing bad code can be a lot of fun. Now here, when I say "bad", I mean something that's functional but completely incoherent to anything but the...
Adobe Analytics Implementation Documentation in 60 seconds
When I was working as a digital analytics consultant, no question quite had the ability to cause belly laughs AND angst as, “Can you send me an updated copy...
roxygen2 3.0.0
We’re pleased to announce a new version of roxygen2. The biggest news is that you can painlessly document your S4 classes, S4 methods and RC classes with roxygen2 –...
“Programming with R” course in Milano (Italy) on January 30-31
Course description This two-day course provides an overview of several advanced R topics, such as: R environments, object oriented programming, functional programming and debugging. Who should attend this course...
Storing package data in custom environments
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...
Data mountains and streams – stacked area plots in R
Below are two functions for producing stacked area plots. The first is the more typical approach where sequential series are stacked on top of another (function: plot.stacked), while the...
Performance of the divide-and-conquer SVD algorithm
The ubiquitous LAPACK library provides several implementations for the singular-value decomposition (SVD). We will illustrate possible speed gains from using the divide-and-conquer method by comparing it to the...
analyze the program for international student assessment (pisa) with r and monetdb
the authoritative source for evaluating educational achievement across nations, the program(me) for international student assessment ranks the math, science, and reading skills of 15-year-olds in more than sixty countries. ...
Summarize statistics by Groups in R & R Commander
R is great at accomplishing complex tasks. Doing simple things with R though takes some effort. Consider the simple task of producing summary statistics for continuous variables over some...
Probabilistic bug hunting
Have you ever run into a bug that, no matter how careful you are trying to reproduce it, it only happens sometimes? And then, you think you've got it, and finally...
Down-Sampling Using Random Forests
We discuss dealing with large class imbalances in Chapter 16. One approach is to sample the training set to coerce a more balanced class distribution. We discuss down-sampling: sample the...
Sentence Drawing: Function vs. Art
I recently was reading the book “Functional Art” and came across the work of Stefanie Posavec. Her Sentence Drawings (click here to see and click here to learn) caught...
Comparing mnlogit and mlogit for discrete choice models
Earlier this weekend (Dec. 7, 2013), mnlogit was released on CRAN by Wang Zhiyu and Asad Hasan ([email protected]) claiming that mnlogit uses “parallel C++ library to achieve fast computation of...
Tim Hortons Density
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...
amazonly associated thanks (& warnin’)
Following a now well-established pattern, let me (re)warn (the few) unwary ‘Og readers that the links to Amazon.com and to Amazon.fr found on this blog are actually susceptible to...
The forestplot of dreams
Displaying large regression models without overwhelming the reader can be challenging. I believe that forestplots are amazingly well suited for this. The plot gives a quick understanding of the...
Fukushima region radiation decrease
Fukushima is still a topic which gets headlines, and somewhere in a comment was a link to actual and historical radiation data: Fukushima prefecture radioactivity measurement map. It...
24 Days of R: Day 8
I saved the data from the last post which shows the percentage of Republican voters in each county. In addition to that column, I also have figures from the...
