Two-Way PERMANOVA (with Vegan-Function adonis) Using Customized Contrasts

August 8, 2011
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(This article was first published on theBioBucket*, and kindly contributed to R-bloggers)

...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.
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