Blog Archives

Longitudinal analysis: autocorrelation makes a difference

October 25, 2011
By
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 … Continue reading →

Read more »

Teaching with R: the switch

October 21, 2011
By

There are several blog posts, websites (and even books) explaining the transition from using another statistical system (e.g. SAS, SPSS, Stata, etc) to relying on R. Most of that material treats the topic from the point of view of i- … Continue reading →

Read more »

Spatial correlation in designed experiments

October 20, 2011
By
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 … Continue reading →

Read more »

On R, bloggers, politics, sex, alcohol and rock & roll

October 19, 2011
By
On R, bloggers, politics, sex, alcohol and rock & roll

Yesterday morning at 7 am I was outside walking the dog before getting a taxi to go to the airport to catch a plane to travel from Christchurch to Blenheim (now I can breath after reading without a pause). It … Continue reading →

Read more »

Large applications of linear mixed models

October 18, 2011
By
Large applications of linear mixed models

In a previous post I summarily described our options for (generalized to varying degrees) linear mixed models from a frequentist point of view: nlme, lme4 and ASReml-R†, followed by a quick example for a split-plot experiment. But who is really … Continue reading →

Read more »

Lattice when modeling, ggplot when publishing

October 17, 2011
By
Lattice when modeling, ggplot when publishing

When working in research projects I tend to fit several, sometimes quite a few, alternative models. This model fitting is informed by theoretical considerations (e.g. quantitative genetics, experimental design we used, our understanding of the process under study, etc.) but … Continue reading →

Read more »

Linear mixed models in R

October 16, 2011
By

A substantial part of my job has little to do with statistics; nevertheless, a large proportion of the statistical side of things relates to applications of linear mixed models. The bulk of my use of mixed models relates to the … Continue reading →

Read more »

Maximum likelihood

October 13, 2011
By
Maximum likelihood

This post is one of those ‘explain to myself how things work’ documents, which are not necessarily completely correct but are close enough to facilitate understanding. Background Let’s assume that we are working with a fairly simple linear model, where … Continue reading →

Read more »

Simulating data following a given covariance structure

October 12, 2011
By

Every year there is at least a couple of occasions when I have to simulate multivariate data that follow a given covariance matrix. For example, let’s say that we want to create an example of the effect of collinearity when … Continue reading →

Read more »

Setting plots side by side

October 11, 2011
By
Setting plots side by side

This is simple example code to display side-by-side lattice plots or ggplot2 plots, using the mtcars dataset that comes with any R installation. We will display a scatterplot of miles per US gallon (mpg) on car weight (wt) next to … Continue reading →

Read more »