27 Feb 2012

Testing the Effect of a Factor within each Level of another Factor with R-Package {contrast}

This is a small example of how custom contrasts can easily be applied with the contrast-package. The package-manual has several useful explanations and the below example was actually grabbed from there.
This example can also be applied to a GLM but I choose to use a LM because the coefficients are more easily interpreted.



8 Aug 2011

Two-Way PERMANOVA (adonis, vegan-Package) with Customized Contrasts

...say you have a multivariate dataset and a two-way factorial design - you do a PERMANOVA and the aov-table (adonis is using ANOVA or "sum"-contrasts) tells you there is an interaction - how to proceed when you want to go deeper into the analysis?
You could, however somewhat tedious, customize contrasts for the PERMANOVA and check for differences between certain level combinations.