I am trying to analyze a model with lme, but I could use some clarification
on the proper syntax for dealing with the nested nature of my experiment.
I have two fixed factors (soil strength = 4 levels; competition = 4 levels)
applied separately to 6 replicate pots per treatment combination (n = 96
pots). Within the pots I took several measurements
on two plants per pot. The
ultimate goal of the experiment is to understand how the two factors affect
plant performance. Although some measurements from the two plants
(subsamples) can be averaged (e.g., height, number of leaves), others that
may be important covariates in the model cannot be averaged (e.g., time
since being galled). So, I need to retain information on individual plants
even though they are obviously subsamples within pot. Any advice would be
appreciated.
Here is a snippet of my data for context: