metacal
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mikemc
Metagenomics calibration R package
It might be convenient to have a function that performs a simple plug-in approach to the the 'reference-species' approach to calibration described by https://github.com/mikemc/differential-abundance-theory. In its simplest form, the function...
Currently the tax info is dropped; but we can keep it in the tax table slot for the numerator and denominator taxon in the tax table just as we do...
An experimental `with_groups()` function was added to dplyr that should be able to do the `mutate_by()` functionality and more.
Can potentially speed up purely in R by doing the matrix algebra and manipulations more thoughtfully. Alternately, could implement in c.
E.g. in `center()`, I must have used dashes which are getting interpreted as markdown bullets
* for both defined and undefined control samples * using the least-squares approach currently used for bias estimation with `center()` * also demonstrate how to do this with `nnet::multinom()`