Have you ever wondered whether the set.seed() function in R has any quirkiness? This analysis was inspired by a Stack Overflow posting by Wolfgang and I incorporate some of his code.For each seed (1-1000, for this analysis), I took the mean and standard deviation of the first 1,000 random ... [Read more...]

Here I will introduce matpow, a package to flexibly and conveniently compute matrix powers.  But even if you are not interested in matrices, I think many of you will find that this post contains much general material on R that you’ll find useful.  Indeed, most of this post will ... [Read more...]

In pipeR 0.4 version, one of the new features is Pipe() function. The function basically creates a Pipe object that allows command chaining with $, and thus makes it easier to perform operations in pipeline without any external operator. In this post, I will introduce how to use this function and some ... [Read more...]

If you're looking for just the right package to solve your R problem, you could always browse through the list of available packages on CRAN. But with almost 6000 entries, that's not going to be the most efficient process. And even then, many very useful packages aren't found on CRAN: there ... [Read more...]

… or Inferring Identity from Observations Let’s assume the following application: A conservation organisation starts a project to geographically catalogue the remaining representatives of an endangered plant species. For that purpose hikers are encouraged to communicate the location of the plant … Continue reading → [Read more...]

Thanks to a blog comment by @arj, I finally ran at least one of the new Rcpp-based through valgrind (resolv) and, sure enough there were a few memory leaks which are now fixed. However, I first ran valgind with a simple test R script that just did library(stats) to ... [Read more...]

I came accross this post on SO, where several solutions to sorting data.frames are presented. It must have been solved a million times, but here's a solution I like to use. It benefits from the fact that sort is an … Continue reading → [Read more...]

The Open Tree of Life project aims to synthesize our combined knowledge of how organisms relate to each other, and make the results available to anyone who wants to use them. At present, the project contains data from more than 4,000 published phylogenies, which combine with other data sources to make ... [Read more...]

I wanted to use R to explore hotel review data. I chose to explore reviews for 3 hotels from Trip Advisor. First, I had to scrape the review data. I have described how I scraped the data here. I used … Continue reading → [Read more...]

When visiting the exhibition hall at JSM 2014, I spoke with people from STEM forums on the Springer booth. The concept of STEM (why STEM? Nothing to do with STAN! Nor directly with Biology. It stands as the accronym for Science, Technology, Engineering, and Mathematics.) is to create a sort of ... [Read more...]

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When working with Node streams, particularly object-mode streams, it's often helpful to be able to inspect a pipeline. The vstream module instruments objects to provide: For all objects: a name: used in debug output and especially useful for data pipelines custom counters: create your own counters… [Read more...]

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Five LA R meetup members will present short talks of what they learned at useR!... [Read more...]

Winston Chang’s “Interactive Graphics with ggvis” talk at useR! 2014 was in many ways a... [Read more...]

by Joseph Rickert I think we can be sure that when American botanist Edgar Anderson meticulously collected data on three species of iris in the early 1930s he had no idea that these data would produce a computational storm that would persist well into the 21st century. The calculations started, ... [Read more...]

I have been looking for an intuitive way to plot flows or connections between states in a process. An obvious choice is a Sankey Plot, but I could not find a satisfactory implementation in R… until I read the riverplot post by January Weiner. His riverplot package does precisely what ... [Read more...]

As I was getting worried about the chances of survival of my current laptop (bought in emergency upon my return from Kyoto!), I decided to use some available grant money to buy a new laptop without stepping through the emergency square. Thanks to my local computer engineer, Thomas, I found ... [Read more...]

A statistical consultant known only as "Stanford PhD" has put together a table comparing the statistical capabilities of the software packages R, Matlab, SAS, Stata and SPSS. For each of 57 methods (including techniques like "ridge regression", "survival analysis", "optimization") the author ranks the capabilities of each software package as "Yes" (... [Read more...]

As separate by-subjects and by-items analyses have been replaced by mixed-effects models with crossed random effects of subjects and items, I've often found myself wondering about the best way to plot data. The simple-minded means and SE from trial-lev... [Read more...]