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.

Adonis (PERMANOVA) - Assumptions

Before you use PERMANOVA (R-vegan function adonis) you should read the user notes for the original program by the author (Marti J. Anderson) who first came up with this method. An important assumtption for PERMANOVA is same "multivariate spread" among groups, which is similar to variance homogeneity in univariate ANOVA.

I'll show why you may draw the wrong conclusions if this assumption is not met:

Multivariate Repeated Measurements with adonis():

Please check the updated code in the comment by Wallace Beiroz, 26 January 2015 at 13:37!

Lately I had to figure out how to do a repeated measures (or mixed effects) analysis on multivariate (species) data. Here I share code for a computation in R with the adonis function of the vegan package. Credit goes to Gavin Simpson providing most of the important pieces of the below code in R-Help.