I currently have an OTU table of 16S Data sequenced through the Illumina MiSeq platform. I also have the table summarized by taxonomy level, so I have counts of each genus for each sample.

I have two sample types: water and fish swabs. They each came from 6 tanks of each treatment (so there's 6 replicates of 3 water treatments: Algae, Clay, and Algae with a switch to Clay after one week-- these are commonly used water additives in aquaculture). The samples were taken three times over the course of 12 days: 3/10, 3/14, and 3/22. 

There were also 3 different crosses of fish, so each genotype had 2 replicates for each treatment.

I'm interested to see how the trends in microbial community structure change over the course of the experiment, organized by sample type, treatment, and genotype, so I was hoping to do principal response curve analysis (I have 3 samples of the original seawater from those time points as a control).

I'm just not sure how to organize my data to do this analysis in R, and the documentation is not very helpful. Any tips would be greatly appreciated!