I'd prefer to have you use *OTU* instead of species, generally through-out this documentation. For example, this section could become:

*All alpha diversity measures accept a vector of counts within a single sample, where each count is, for example, the number of observations of a particular Operational Taxonomic Unit, or OTU. We use the term "OTU" here very loosely, as these could be counts of any type of feature/observation (e.g., bacterial species).*