creating rarefaction curves
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Entering edit mode
8.6 years ago
Phil S. ▴ 700

Hiho

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)

R metagenomics DNA-seq • 19k views
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Entering edit mode
8.6 years ago

My quite naive suggestion is to estimate the richness with some estimator like Chao1 (should be in Vegan package), then extrapolate your richness curve to get 90% of estimated diversity and check for the sample size. See iNEXT R package for details on extrapolating rarefaction curves.

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Entering edit mode

Since I already calculate chao and the improved chao which was just recently published (along with the variance etc...) I will definitely have a look into that!

Thank you so much!

edit: Thanks for the suggestion. It is exactly what I was looking for!!!!!!!