Category: r (Page 7 of 20)

Using Processing and R together (in OS X)

2013-12-20 / Luis

I wanted to develop a small experiment with a front end using the Processing language and the backend calculations in R; the reason why will be another post. This post explained the steps assuming that one already has R and Processing installed:

Install the Rserve package. This has to be done from source (e.g. using R CMD INSTALL packagename).
Download Rserve jar files and include them in the Processing sketch.
Run your code

Excel, fanaticism and R

2013-12-17 / Luis

This week I’ve been feeling tired of excessive fanaticism (or zealotry) of open source software (OSS) and R in general. I do use a fair amount of OSS and pushed for the adoption of R in our courses; in fact, I do think OSS is a Good Thing^TM. I do not like, however, constant yabbering on why using exclusively OSS in science is a good idea and the reduction of science to repeatability^‡ and computability (both of which I covered in my previous post). I also dislike the snobbery of ‘you shall use R and not Excel at all, because the latter is evil’ (going back ages).
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Gratuitous picture: just different hardware (Photo: Luis, click to enlarge).

Flotsam 13: early July links

2013-07-10 / Luis

Man flu kept me at home today, so I decided to do something ‘useful’ and go for a linkathon:

Ed Yong discusses the effect of subject expectations in psychology experiments Nice Results, But What Did You Expect? At the beginning there was another article on The placebo phenomenon, and another one on The placebo defect.
A googleVis tutorial to create Hans Rosling-type graphs from R.
Google’s Python Class is material for an intensive 2-day course on Python.
An opinion piece on Calculus and statistics by Daniel Kaplan, on teaching a different version of your typical introductory calculus course, so it is useful for statistics. He goes as far as teaching calculus using R. There is more information in Project MOSAIC.
Nice graphs on what happened to Asiana Airlines flight 214. I didn’t know there was so much available data for a specific flight.
Biased and Inefficient, Thomas Lumley’s personal statistics blog (he insists that posting 75% of Statschat is not enough to qualify as personal). You may know Thomas from the survey package (or a few others).
If you are a postgrad student in New Zealand you can apply for a NeSI (New Zealand eScience Infrastructure) postgraduate allocation to access high performance computing facilities.
My previous post the USA versus Western Europe comparison of GM corn was the first time that I received more traffic from Facebook than from R-bloggers. Five hundred readers in total.

Over and out.

My take on the USA versus Western Europe comparison of GM corn

2013-07-04 / Luis

A few days ago I came across Jack Heinemann and collaborators’ article (Sustainability and innovation in staple crop production in the US Midwest, Open Access) comparing the agricultural sectors of USA and Western Europe^‡. While the article is titled around the word sustainability, the main comparison stems from the use of Genetically Modified crops in USA versus the absence of them in Western Europe.

I was curious about part of the results and discussion which, in a nutshell, suggest that “GM cropping systems have not contributed to yield gains, are not necessary for yield gains, and appear to be eroding yields compared to the equally modern agroecosystem of Western Europe”. The authors relied on several crops for the comparison (Maize/corn, rapeseed/canola^{see P.S.6}, soybean and cotton); however, I am going to focus on a single one (corn) for two reasons: 1. I can’t afford a lot of time for blog posts when I should be preparing lectures and 2. I like eating corn. Continue reading

Analyzing a simple experiment with heterogeneous variances using asreml, MCMCglmm and SAS

2013-05-17 / Luis

I was working with a small experiment which includes families from two Eucalyptus species and thought it would be nice to code a first analysis using alternative approaches. The experiment is a randomized complete block design, with species as fixed effect and family and block as a random effects, while the response variable is growth strain (in \( \mu \epsilon\)).

When looking at the trees one can see that the residual variances will be very different. In addition, the trees were growing in plastic bags laid out in rows (the blocks) and columns. Given that trees were growing in bags siting on flat terrain, most likely the row effects are zero.
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