Compare the convergence of the model using two different set of parameters for the competition effect using Basal area:

  • sim1: \(lower\) and \(beta\) parameters varying; \(mid = 20\), \(upper = 1\)
  • sim2: \(lower\) and \(mid\) varying; \(beta = 0.3\), \(upper = 1\)

Rhat

Divergent transitions

Density plot of each parameter by species id

Data distribution

Size, temperature, precipitation and competition effect

Predictions

Out-of-bag predictions

Mean squared error (MSE) of out-of-bag predictions

Density distribution draws from the posterior distribution (\(n = 500\)) can be compared with the MSE values using the random forest methods (vertical bars). Furthermore, I added the sim_full MSE when running the random forest with all non-correlated variables to get the maximum explicability from data.

Rsquared

Rsquared values draw from the posterior distribution is calculated using the Gelman et al. 2018 definition. Like MSE, the \(R^{2}\) can be compared with the ones from the random forest using the same variables along with the full model (sim_full). However, the \(R^{2}\) of the random forest is calculated using the classical equation.

Sampling time