December 2012

Anaerobic Stress in Seeds – A Chemical Similarity Network Story

December 31, 2012 | 0 Comments

The chemical similarity network or CSN is a great tool for organizing biological data based on known biochemistry or chemical structural similarity. Here is an example CSN for visualizing metabolomic  changes (measured via GC/TOF) due to anaerobic stress in germinating seeds. In this network edges are formed for chemical ... [Read more...]

Getting Genetics Done 2012 In Review

December 31, 2012 | 0 Comments

Here are links to all of this year's posts (excluding seminar/webinar announcements), with the most visited posts in bold italic. As always, you can follow me on Twitter for more frequent updates. Happy new year!New Year's Resolution: Learn How to Code... [Read more...]

The forward (explicit) Euler method

December 31, 2012 | 0 Comments

The forward (explicit) Euler method is a first-order numerical procedure for solving ODEs with a given initial value. The forward Euler method is said to be the simplest and most obvious numerical ODEs integrator. In fact, the simulation using the forward Euler only … Continue reading → [Read more...]

Nested loops with mapply

December 31, 2012 | 0 Comments

So as I sink deeper into the second level of R enlightenment, one thing troubled me. “lapply” is fine for looping over a single vector of elements, but it doesn’t do a nested loop structure. These tend to be pretty ubiquitous for me. I’m forever doing the same ... [Read more...]

Top Posts of 2012

December 31, 2012 | 0 Comments

This has been a great year for my blog. I've seen tremendous growth in my subscribers. I look forward to engaging with and learning from my followers in 2013 and I plan to offer valuable content in return. If you're interested in following along, you can quickly subscribe via RSS or ... [Read more...]

How odd was the UEFA draw?

December 31, 2012 | 0 Comments

I've been away for some time without closely following the media, and without significant internet access. When such a period is over it takes some time to regain momentum. Thus my short exit poll series will be continued in 2013. For now I'm still sor... [Read more...]

STL random_sample

December 31, 2012 | 0 Comments

An earlier post looked at random shuffle for permutations. The STL also supports creation of random samples. Alas, it seems that this functionality has not been promoted to the C++ standard yet — so we will have to do with what is an extensions ... [Read more...]

Modeling in R with Log Likelihood Function

December 30, 2012 | 0 Comments

Similar to NLMIXED procedure in SAS, optim() in R provides the functionality to estimate a model by specifying the log likelihood function explicitly. Below is a demo showing how to estimate a Poisson model by optim() and its comparison with glm() result. [Read more...]

Tips for R Package Creation

December 30, 2012 | 0 Comments

I’m being tortured by the mistakes of my past self. I think I’ve made most every mistake possible in creating a package and I want to go back in time and tell year ago me all I know now. But … Continue reading → [Read more...]

2012 in review by The

December 30, 2012 | 0 Comments

Here is a 2012 annual report for this blog produced by The My top post this year based on number of views are R-Uni (A List of Free R Tutorials and Resources in Universities webpages) 29 COMMENTS February 2012 R Style Guide 7 COMMENTS June 2012 Click here to see the complete report. ... [Read more...]

Pearson’s r: Not a good measure of electoral persistence

December 30, 2012 | 0 Comments

Pearson’s product-moment correlation, \(r\), is an incredibly useful tool for getting some idea about how two variables are (linearly) related. But there are times when using Pearson’s \(r\) is not appropriate and, even if linearity and all other assumptions hold, … Continue reading → [Read more...]

RcppClassicExamples 0.1.1

December 30, 2012 | 0 Comments

Yesterday's initial upload of RcppClassicExamples was lacking a versioned Depends: to prevent builds on older versions of R. This has been added in a new upload 0.1.1. We also added a NEWS file (see below); no code changes were made. Changes in ver... [Read more...]

National idenftification number: Finland

December 30, 2012 | 0 Comments

The Finnish Social Security number (FSSn) is a common variable in a Finnish population based study. Within FSSn are individuals birthday, and gender. We can also check if the FSSn correct because it has a check digit. If the data doesn't have birthday ... [Read more...]

STL random_shuffle for permutations

December 30, 2012 | 0 Comments

The STL also contains random sampling and shuffling algorithms. We start by looking at random_shuffle. There are two forms. The first uses an internal RNG with its own seed; the second form allows for a function object conformant to the STL’s re... [Read more...]

Update to Graphing Non-Proportional Hazards in R

December 30, 2012 | 0 Comments

Update 1 February 2013: I've moved all of the functionality described in this post into an R package called simtvc. Have a look. It is much easier to use. This is a quick update for a previous post on Graphing Non-Proportional Hazards in R. In the previous post I showed how to ...
[Read more...]

Spirograph with R

December 30, 2012 | 0 Comments

Just had to figure out how to replicate this old toy of mine with R! I had no idea how long it's been around:Read more » [Read more...]

An R wish list for 2013

December 29, 2012 | 0 Comments

First go and read An R wish list for 2012. None of the wishes came through in 2012. Fix the R website? No, it is the same this year. In fact, it is the same as in 2005. Easy to find help? Sorry, next year. Consistency and sane defaults? Coming soon to a ... [Read more...]
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