Category: asreml

  • Coming out of the (Bayesian) closet

    Coming out of the (Bayesian) closet

    Until today all the posts in this blog have used a frequentist view of the world. I have a confession to make: I have an ecumenical view of statistics and I do sometimes use Bayesian approaches in data analyses. This is not quite one of those “the truth will set you free” moments, but I’ll…

  • Multivariate linear mixed models: livin’ la vida loca

    Multivariate linear mixed models: livin’ la vida loca

    I swear there was a point in writing an introduction to covariance structures: now we can start joining all sort of analyses using very similar notation. In a previous post I described simple (even simplistic) models for a single response variable (or ‘trait’ in quantitative geneticist speak). The R code in three R packages (asreml-R,…

  • Covariance structures

    Covariance structures

    In most mixed linear model packages (e.g. asreml, lme4, nlme, etc) one needs to specify only the model equation (the bit that looks like y ~ factors…) when fitting simple models. We explicitly say nothing about the covariances that complete the model specification. This is because most linear mixed model packages assume that, in absence…

  • Longitudinal analysis: autocorrelation makes a difference

    Longitudinal analysis: autocorrelation makes a difference

    Back to posting after a long weekend and more than enough rugby coverage to last a few years. Anyway, back to linear models, where we usually assume normality, independence and homogeneous variances. In most statistics courses we live in a fantasy world where we meet all of the assumptions, but in real life—and trees and…

  • Spatial correlation in designed experiments

    Spatial correlation in designed experiments

    Last Wednesday I had a meeting with the folks of the New Zealand Drylands Forest Initiative in Blenheim. In addition to sitting in a conference room and having nice sandwiches we went to visit one of our progeny trials at Cravens. Plantation forestry trials are usually laid out following a rectangular lattice defined by rows…