TestMatchedControlMixedModel: Create and test a mixed effect model between two sample types...
In eclarke/SarcoidMicrobiome: Figures for the Clarke et al sarcoid microbiome paper

Description Usage Arguments

Create and test a mixed effect model between two sample types and study groups (e.g. BAL and prewash, tissue and paraffin), where the interaction term for the model is the coefficient of interest.

1 2	TestMatchedControlMixedModel(agg, grouping.var = "OriginatingSampleID", tax.level = "Genus", sparsity = 0.1)

`agg`	an agglomerated data frame; ensure the StudyGroup and SampleType levels are ordered correctly (i.e. interesting ones last)
`grouping.var`	the column defining the sample/control grouping
`tax.level`	the taxonomic level to test; lower levels will be summed
`sparsity`	the proportions of zeros below which a taxa will be skipped