Palimpsest

Evolving notes, images and sounds by Luis Apiolaza

Category: MCMCglmm

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

2013-05-17 /

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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Gratuitous picture: 3000 trees leaning in a foggy Christchurch day (Photo: Luis).

When R, or any other language, is not enough

2012-12-15 /

This post is tangential to R, although R has a fair share of the issues I mention here, which include research reproducibility, open source, paying for software, multiple languages, salt and pepper.

There is an increasing interest in the reproducibility of research. In many topics we face multiple, often conflicting claims and as researchers we value the ability to evaluate those claims, including repeating/reproducing research results. While I share the interest in reproducibility, some times I feel we are obsessing too much on only part of the research process: statistical analysis. Even here, many people focus not on the models per se, but only on the code for the analysis, which should only use tools that are free of charge.

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Surviving a binomial mixed model

2011-11-12 /

A few years ago we had this really cool idea: we had to establish a trial to understand wood quality in context. Sort of following the saying “we don’t know who discovered water, but we are sure that it wasn’t a fish” (attributed to Marshall McLuhan). By now you are thinking WTF is this guy talking about? But the idea was simple; let’s put a trial that had the species we wanted to study (Pinus radiata, a gymnosperm) and an angiosperm (Eucalyptus nitens if you wish to know) to provide the contrast, as they are supposed to have vastly different types of wood. From space the trial looked like this:
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