Question: creating rarefaction curves
gravatar for Phil S.
4.7 years ago by
Phil S.660
Stuttgart, Germany
Phil S.660 wrote:


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 • 12k views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 4.7 years ago by Phil S.660
gravatar for mikhail.shugay
4.7 years ago by
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.

ADD COMMENTlink written 4.7 years ago by mikhail.shugay3.3k

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!!!!!!!

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by Phil S.660
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2482 users visited in the last hour