creating rarefaction curves

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

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updated 4.7 years ago by Ram

• written 12.1 years ago by Phil S.

1 answer

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.

• 1 views • link

updated 4.7 years ago by Ram

• written 12.1 years ago by mikhail.shugay

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!!!!!!!

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written 12.1 years ago by Phil S.