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## Help analyzing Split Plot with SubPlot in Fit Model with ANOVA for each factor.

I have an experiment where I grew plants on three separate benches in a gh and measured the response of shoots harvested on flowering time.

My whole plot factor is light (3 levels) and my blocking factor is the benches (1-3)

On each of these benches,  each light level is present (randomized on each bench) (1-3)  So I have replication on each bench. With each light level treatment replicated 3 times.

Each row represents the benches (1-3) with each light level present on each bench.

 Light level 3 Light level 2 Light level 1 Light level 2 Light level 1 Light Level 3 Light level 1 Light level 3 Light Level 1

Within each of these light levels on each of these benches, I had 36 plants in which I was applying a chemical at 4 different rates:

Split-plot factor: Chemical application rate: 4 levels.

With 36 total plants, there were 9 plants per chemical treatment in each light level.

Sub plot factor: Harvest position

Those 9 plants receiving a specific chemical treatment were then subdivided into where I was harvesting shoots.

I  have a base location on the plant called primary stalk nodes 1, 2, or 3 and harvested the actual shoots that arose from each of the primary nodes at two different secondary node positions, 2 or 3.

So, 3 of the 9 plants were harvested at primary nodes 1-3 at sec 2 shoots that arose from each of the primary's.

the remaining 3 plants of the 9 were also harvested on primary nodes 1-3 but I took the 3rd node shoot that arose from each of the primary nodes. So I have combinations of node positions for harvesting shoots.

 Primary Secondary 1 2 2 2 3 2 1 3 2 3 3 3

I am very confused and I do not know how to set my data up in JMP. I have been reading lots of threads that say I need to nest my light by tables and it is a random effect, etc, etc. but I am still not sure what is the correct way to set it up and what attributes are associated with each factor.

Can someone explain how I set this up and which model to run?

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Super User

## Re: Help analyzing Split Plot with SubPlot in Fit Model with ANOVA for each factor.

Looks like you have what I would call a "blocked split-split-plot" experiment, which is a little nuts.  If I understand your problem correctly, you would need to do the following in Fit Model:

2. Add a "Whole Plot" block as another random effect.  This should group together data points from the same light level on the same bench.

3. Add a "Subplot" block as another random effect, which groups together data points from the same combination of bench, light level, and chemical application rates.

4. Add a "Subsubplot" block as another random effect, which should uniquely identify individual plants.

5. Add all your fixed effects (Light Level, Chemical Application Rate, and Harvest Position, any desired interaction terms, etc.).