I am looking for help to create a model for the following data:
I'd like to understand if the abundance of a certain microbial group (dependent continuous variable QUANTITY) found in soils is been affected by land-use, seasonality and their interaction. For each land-use (factor LAND-USE with 2 levels: forest and pasture), I have 3 different sites (factor SITE with 6 levels: F1, F2, and F3 for FOREST and P1, P2, and P3 for PASTURE). At each site, I collected soil samples in 5 points (factor POINT). Therefore, POINT is nested in SITE and SITE is nested in LAND-USE. In the end, I have 5 points per site and 15 per land-use, totaling 30 points in the study. However, each point was sampled twice (factor SEASON with 2 levels: DS and RS), during the dry and rainy seasons.
My dataframe looks like this:
SEASON LAND-USE SITE POINT QUANTITY
DS FOREST F1 F1_1 300.00
DS FOREST F1 F1_2 330.00
DS FOREST F1 F1_3 530.00
DS FOREST F1 F1_4 670.00
DS FOREST F1 F1_5 80.00
DS FOREST F2 F2_1 600.00
DS FOREST F2 F2_2 630.00
DS FOREST F2 F2_3 780.00
DS FOREST F2 F2_4 900.00
DS FOREST F2 F2_5 1,000.00
RS PASTURE P3 P3_1 800.00
RS PASTURE P3 P3_2 730.00
RS PASTURE P3 P3_3 980.00
RS PASTURE P3 P3_4 550.00
RS PASTURE P3 P3_5 700.00
I am not interested in the site or point itself. I just need to know the effects of land-use and seasonality. However, I am not sure how to code site and point in the error term using AOV.
For example, what's the difference in the following codes? I know this is a very basic question, but even after reading a series of tutorials, I still do not understand which one I should choose in this case.
aov(QUANTITY ~ Season * Land-use + Error(Site), archaea)
aov(QUANTITY ~ Season * Land-use + Error(Point), archaea)
aov(QUANTITY ~ Season * Land-use + Error(Site/Point), archaea)
I would appreciate any advice. If there is anything that I should clarify, please let me know!