[R-sig-ME] Species as both fixed and random effect

[Liliana D'Alba Altamirano]

I have a question about the use of a factor as both fixed and random effect.  Specifically, I want to test the effects of an experimental treatment and the species from which the samples originate on the response variable "y".

I have seven different species with about 10 samples from each.  On one hand I want to be able to make inferences about the differences in "y" between different species, but I also want to look at the variance among the values of "y" at different species (random). In addition, two separate reviewers have explicitly asked for species to be included as random effect to account for the non-independence among data from different species.


So, my model looks like this:


y ~ treatment + species + (1|species)


The question is whether this is an example of statistical malpractice or it is correct to do it.

I am aware of the discussion about this topic posted here:

https://stat.ethz.ch/pipermail/r-sig-mixed-models/2014q3/022365.html

in which Thierry Onkelinx mentioned that it is ok to specify a factor as fixed and random effect but only when it is treated as continuous (fixed) variable.

However, that did not fully answer my question and unlike Year (which can be used as continuous variable), it does not make sense to treat Species as continuous just so the model produce good estimates.


Thank you, I appreciate your help.


Liliana

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