I have the following data: Pine Forest Biomass ~ Age | Plot:

enter image description here

Each black curve represents whole-plot biomass for each individual plot

I want to formally examine this trend using mixed effects model (using lme4 function in R).

Thus far, I created a mixed model with random intercepts and slopes:

lme4(Biomass ~ I(Age - 51) + (1 + I(Age - 51) | Plot), data = dat, REML = F)

I added additional predictors to the model to better explain some of the trend:

lmer(Biomass ~ I(Age - 51) * LossRate + I(Age - 51) * I(scale(PineStems)) + (1 + I(Age - 51)|Plot),data = dat, REML = F)
  • where LossRate is biomass lost per year due to mortality and PineStems are the number of pine stems in a given plot in a given year.

This model seems to perform just fine (based on significant 95% bootstrapped CIs for coefficient estimates and for CIs for the whole model). However, it doesn't account for the downward curve you can see in some plots.

I was thinking I could account for this curve by incorporating a quadratic term for age (i.e., I(scale((Age - 51)^2)) [we'll call it "Age^2"]

However, I'm not sure the best way to do this....

I'm pretty sure that I need to add a random effect for Age^2 since only some plots have the curve, but do I also need to add Age^2 as a fixed effect?

  • Adding it as both a fixed and random effect improves the AIC of the model a lot (vs. no Age^2 term), but adding just the random Age^2 (without Age^2 as a fixed effect) improves the model even more.

  • In general, does adding a squared "time" predictor as a random effect but not adding it as a fixed effect make sense?? (read: "Can I do that??")

Further, I expect the largest impact of PineStems on the model as being the main driver causing the downward slope in biomass in mature plots. In other words, I mostly expect PineStems to drive the Age^2 term (so that as PineStems decreases to a certain point, the trend line turns downward). How can I additionally add that to my model? Just simply by creating an interaction (Age^2 * PineStems)? Or does the model make this connection on its own?


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