Abundance classification

[TuomasBorman]

This PR implements abundance classification that is introduced in this paper:

Sizhong Yang, Matthias Winkel, Dirk Wagner, Susanne Liebner, Community structure of rare methanogenic archaea: insight from a single functional group, FEMS Microbiology Ecology, Volume 93, Issue 11, November 2017, fix126, https://doi.org/10.1093/femsec/fix126

New functions include:

• getAbundant(): taxa above abundance threshold
• getLowAbundant(): taxa below abundance threshold (and between conditionally & permanently rare thresholds)
• getPermanentlyRare(): taxa below abundance threshold and below permanently rare threshold
• getConditionallyRaret(): taxa below abundance threshold and above conditionally rare threshold

TODO:

• Update documentation
• Clean code and check that everything works
• Add unit tests
• Consider names getPermanentlyLowAbundant() and getConditionallyLowAbundant(). They are longer but more distinct from getRare() which is based on prevalence.

[antagomir]

Is getLowAbundant needed if it is just a complement of getAbundant?

[TuomasBorman]

• Abundant taxa: Taxa with an average abundance exceeding abundant.th.

• Low abundant / rare taxa: Taxa with an average abundance not exceeding abundant.th. Optionally, if specified, they must also satisfy the condition:
  condition.th >= (abundance_max / abundance_min) > permanent.th.

• Conditionally rare taxa (CRT): Taxa with an average abundance not exceeding abundant.th and with a maximum-to-minimum abundance ratio (abundance_max / abundance_min) greater than condition.th.

• Permanently rare taxa (PRT): Taxa with an average abundance not exceeding abundant.th and with a maximum-to-minimum abundance ratio (abundance_max / abundance_min) less than or equal to permanent.th.

In the simplest case it is complement, but in the article they further classified the rare taxa

[antagomir]

Is the Shade et al. manuscript also taken into account?

[TuomasBorman]

See: microbiome/miaTime#103