MixSIAR
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Calculating the Bayesian R-squared
I submitted my Isotope paper for review and one comment was regarding my MixSIAR models and how well the top model performed. They suggested I calculate an R2 value like one might if you used AIC to pick the best model and then describe how that current model fits that particular data. One issue I have with my data is that my "best" model isn't much better than any of the other models above the Null. the difference in the SE of LOOic overlap `
Model | Covariate(s) | LOOica | se_LOOicb | dLOOicc | se_dLOOicd |
---|---|---|---|---|---|
13 | Harvest method by Age | 282.2 | 29 | 0 | NA |
5 | Harvest method | 284.9 | 30.4 | 2.7 | 7.5 |
3 | Location | 285.6 | 28 | 3.4 | 8.3 |
7 | Harvest method by Sex | 285.9 | 30.5 | 3.7 | 8.3 |
6 | Harvest method by Location | 286.7 | 29.9 | 4.5 | 7 |
2 | Sex | 288.1 | 28.8 | 5.9 | 10.1 |
1 | Null | 288.7 | 28.5 | 6.5 | 9.2 |
Though Im not sure if I am phrasing that correctly. The difference in SE is like confidence intervals and therefore because those overlap, we can't distinguish really the "best". Anyway, The rest of my paper is predicated upon the fact that although the others have some explanatory value, harvest method is clearly important and we proceed with just exploring the patters observed from age class. So, because of that, the reviewer wants to see how well that one model is doing and is asking for an R-squared value type indication.
Has anyone done this yet? I found https://avehtari.github.io/bayes_R2/bayes_R2.html and the associated paper https://www.tandfonline.com/doi/full/10.1080/00031305.2018.1549100 but do not know how to write the code to incorporate this into the example coding from MixSIAR. unless Ive missed it somewhere. Otherwise, I don't know how to tell this reviewer R2 isn't exactly transferrable to Bayesian processes. R2 evaluates a particular point and doesn't deal with uncertainty