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Old 07-15-2014, 01:30 AM   #1
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Location: Stuttgart, Germany

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Posts: 192
Default rarefaction curves and simulation


i want to create a rarefaction curve using R i.e. vegan {rearecurve/speccaccum}.

This worked out quite well (please see here)

Anyways, as you can see in the figures the curves don't reach saturation. So I know that i have to kind of fit or simulate the missing data but this is exactly the problem. How can I produce a fit or something similar that shows me how large my sample has to be to reach saturation in discovered species?

Thanks for your time and help!

ps. code:

(raremax <- min(rowSums(t(species))))
Srare <- rarefy(t(species), raremax)
plot(specnumber(t(species)), Srare, xlab = "Observed No. of Species", ylab = "Rarefied No. of Species")
abline(0, 1)
rarecurve(t(species), step = 20, sample = raremax, col = "blue", cex = 0.6)

(crosspost on biostars)
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