Question: creating rarefaction curves
2
4.3 years ago by
Phil S.660
Stuttgart, Germany
Phil S.660 wrote:

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)

dna-seq metagenomics R • 11k views
modified 19 months ago by Biostar ♦♦ 20 • written 4.3 years ago by Phil S.660
4
4.3 years ago by
mikhail.shugay3.3k
Czech Republic, Brno, CEITEC
mikhail.shugay3.3k wrote:

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.

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!!!!!!!