I'm currently running into an issue where I am attempting to calculate diversity of macroinvertebrates in a sample. Most are ID'd to the level of genus, but a few are too small or damaged to be ID'd beyond family. When calculating total taxa richness or using the Shannon Diversity Index, what would be the best way to incorporate all of this data? If I use only the genus level ID's then I will be losing all of the family level specimens which will throw off calculations as that lowers the total number of specimens in the sample and may underrepresent the diversity of the sample. However, if I count the family level specimens there is a risk that some of those are in the same genera as other specimens which would artificially inflate the diversity value of the sample.

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