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Abundance classification #664
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Is |
In the simplest case it is complement, but in the article they further classified the rare taxa |
Is the Shade et al. manuscript also taken into account? |
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 thresholdgetLowAbundant()
: taxa below abundance threshold (and between conditionally & permanently rare thresholds)getPermanentlyRare()
: taxa below abundance threshold and below permanently rare thresholdgetConditionallyRaret()
: taxa below abundance threshold and above conditionally rare thresholdTODO:
getPermanentlyLowAbundant()
andgetConditionallyLowAbundant()
. They are longer but more distinct fromgetRare()
which is based on prevalence.