I designed my experiment in a way that I thought would present me with options for analysis, but I'm starting to wonder if one of the options would be considered pseudoreplication.
The experiment was like this:
I work with 2 mussel species (Z and Q).
I put 4 of each species in a pipe in the river (each of the four got their own little chamber inside).
Each pipe had a baffle on the front and back to change water flow into and out of the pipe
I made four baffle types (A, B, C, D), with the intent that each one would allow faster/more water flow than the previous (ie A
I grouped one of each pipe type together to make a replicate (right?) and attached these replicates to a cinderblock
There were 10 cinderblocks total
I put these underwater, cleaned them every two weeks, and took pre- and post- measurements of mussel body size, and also got attachment strength.
The pipes looked like this So, option 1 is:
I could just analyze the data as a 4x2 ANOVA, with the pipe type (A, B, C, D) vs. species (Z vs Q) with something like body length as the response variable (I have others), and Cinderblocks as a random blocking factor.
BUT! in each pipe, I also included a hard plaster block that dissolved over time under water, ostensibly with higher dissolution due to increased water flow. I checked to see if the pipe baffle had any effect with a one way ANOVA (response variable = amount dissolved; four pipe types) and I found that the baffles basically did what I wanted them to (A
Therefore option 2 is:
I could do a regression/ANCOVA using these plaster blocks, with species as the factor, plaster mass lost as the covariate, and body length as the response variable, with cinderblocks again acting as a random blocking factor.
My questions are:
1) is the second option pseudoreplication, because there is only one measure of flow per pipe, but 4 mussels of each species per pipe?.
2) if it's not pseudoreplication, how do I tell if I should go with the ANOVA or ANCOVA?
I'm using JMP for the analysis, which can't do GLMM unfortunately. Any help would be appreciated.