I used an R script provided by Emma to cluster each silo.
The scree plots for each silo are:
I choose four clusters for each silo so that they could be better compared between one another. It was somewhat difficult to determine cluster numbers because the first component was so much larger than any others…
The plots are comparing the first measured day of the experiment with the last.
Initially I choose only 3 clusters for Silo 2. The comparison between 3 and 4 clusters for silo 2:
Here is Silo 3 followed by Silo 9 with 4 clusters:
I’m working next on Eigen vectors (I’m having a problem getting R to read my data as numeric) and incorporating the cluster assignment into the excel spreadsheet as a tag.