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

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

When R, or any other language, is not enough

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… Continue reading When R, or any other language, is not enough

Multisite, multivariate genetic analysis: simulation and analysis

The email wasn't a challenge but a simple question: Is it possible to run a multivariate analysis in multiple sites? I was going to answer yes, of course, and leave it there but it would be a cruel, non-satisfying answer. We can get a better handle of the question if we use a simple example;… Continue reading Multisite, multivariate genetic analysis: simulation and analysis

Overlay of design matrices in genetic analysis

I've ignored my quantitative geneticist side of things for a while (at least in this blog) so this time I'll cover some code I was exchanging with a couple of colleagues who work for other organizations. It is common to use diallel mating designs in plant and tree breeding, where a small number of parents… Continue reading Overlay of design matrices in genetic analysis

Split-plot 2: let’s throw in some spatial effects

Disappeared for a while collecting frequent flyer points. In the process I 'discovered' that I live in the middle of nowhere, as it took me 36 hours to reach my conference destination (Estoril, Portugal) through Christchurch, Sydney, Bangkok, Dubai, Madrid and Lisbon. Where was I? Showing how split-plots look like under the bonnet (hood for… Continue reading Split-plot 2: let’s throw in some spatial effects