In a semi-controlled experiment, seeds were sown in about 20 boxes, associated with 3 types of soil. A few months later, the morphological characteristics of the shoots were measured. We would like to study the effect of the type of Soil on these Morphological characteristics but it appears that there is some variability in these characteristics between shoots sown in different boxes with the same type of soil.
Is it correct to consider this data as nested and analyse it by means of a linear mixed model like:
Morphological characteristics ~ Soil + 1|Box
Or is there any other solution to deal with this Box variable, which is a confounding variable because each Box is only associated with one type of Soil.