I am new to JMP so am hoping you can help!
My experiment was a randomised complete block 2 x 2 factorial design with two levels of supplementary additives. A total of 480 individuals were blocked into pens of 5 (pen acts as the experimental unit, not individual), and pens within a replicate were alloacted to one of the 4 dietary treatments. I had 24 replicates in total, but the experiment was conducted over two batches, the first 240 individuals (12 reps) in february and the second batch of 240 indivudals (12 reps) in April. I therefore need to account block for rep and account for batch.
I just want to check i am doing the ANOVA correctly, in the 'construct model effects' box i have my two factors, their interaction, Batch and rep, is this correct? However, when i do this batch looses its DF (as in the picture) so im not sure what to do?
I also need to add a covariate for start weight for some of the analysis, does this also go in the 'construct model effects' box or should continous covariates go in another box?
If I understand correctly - and there is every chance that I do not! -
I'm not sure why rep needs to be included as an effect. Rep seems to me to be an artificial construct here.
Is there any reason to expect a systematic difference between reps. I.e. some reason why all pens within a rep would experience some effect that would change their overall response relative to another rep? Is each rep all within a different building? Or was each rep started at a different time point? Or each rep is from a different parent stock (dont know if that is possible in nutrition trials but I'm jsut tyring to think of possible examples!)?
If there is no reason for a systematic effect of rep then I dont think it needs to be in the model.
If it should be in the model then I would think it should be in there as a random effect.
Similarly "batch" should be a random effect.
One reason for using random effects is that they consume less degrees of freedom.
I hope that helps. Let me know if I have got something wrong in my understanding or if you have questions.
Okay, I think I see what has happened there. Specifying nested effects is not trivial!
I think what you have there is Batch nested within Rep - Batch[Rep]. Whereas you want Rep nested within Batch - Rep[Batch]. I think you should also have Batch as an effect. And both Rep[Batch] and Batch should be random effects.
There is an example of a nested random effects model in the JMP Documentation here. It is from a very different industry and appliction but it should make sense.