The Goal Determine if the abundance of ectos differ between sites.
The set up The data is percent abundance of ectomycorrhizal fungi from soil samples. There are ten soil samples per plot and there are three plots per site, except for the last site which only has one plot ( I know, bad design....). Finally there are three sites. If I have to remove the last site with one plot I can. Currently I am running my model with plot nested within site. However I believe I don't have enough levels within the nested factor to do this? My current model is
m2<-glmmTMB(percent~site+(1|site/plot),data=percentabund,family=beta_family(link = "logit"))
I could change the nested random factor plot to a fixed factor?
m2<-glmmTMB(percent~site+(1|plot),data=percentabundunknown,family=beta_family(link = "logit"))
Have I specified the model correctly?
How do I account for (the unbalanced design)?
I really appreciate any help.