To filter out species that appear fewer than 50 times in your database (filter our rare species) you would first make a list of species and count them, then you would type in what command?
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Please provide a reproducible example. – Phil Apr 25 '20 at 03:08
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Welcome to SO! We need ti understand the structure of your data and clear information about your expected output. A reproducible sample would help us on that. Refer this to know how to get a reproducible sample. https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example – Mohanasundaram Apr 25 '20 at 03:47