rarefy_sample_explicit function

[mobiodiv]

rarefy_sample_explicit function

[rueuntal]

Yeah we are perhaps sacrificing some readability for efficiency here. This is counting the number of species in a treatment accumulating with samples (plots). The abundances are converted to 0's & 1's - 0 for PRESENCE and 1 for ABSENCE within a plot, the reverse of what we'd normally expect. Then the cumulative presence/absence (rich here) is obtained by taking the column product, going down one row at a time. So if one species is present in any of the rows above the focal row, we'd get a product of zero. If it's absent all the way down, we'd get a 1. Then the last line computes the richness for 1 plot, 2 plots, ... (the rowSums part), and converts the number back into true richness.

Let me know if that doesn't make sense.