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All the ecoPD code looks fantastic, I ran it to confirm the values match the original data, and they match, no problems.
I noticed that in the evenness.R code (.scheiner function) that the abund=FALSE option fails for me. It appears to do so at L402 ("data$comm <- as.numeric(data$comm > 0)") since this causes the next line 405 (output <- numeric(nrow(data$comm)) ) to produce an error, since you have lost the matrix structure for data$comm.
I won't edit the code, in case there's a particular way you want to adjust it, but if you can't replicate the error, let me know.
Please have a quick final test of the code. I think it works, but you (Caroline) are the one who knows best :D
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