To determine whether the sampling was sufficient, I plotted rarefaction curves for four sites using rarecurve() function in R vegan package. Seems like the curves have not yet "converged" (i.e. reached asymptote), and each site has different sample size. I would like to add fittings on the curves, so that I can comment on how similar the sites are in terms of their need for further sampling. I assume then I would also be able to comment on which site is subset of which.
One way to do this I guess was explained in this paper (http://www.wsl.ch/info/mitarbeitende/wohlgemu/pdf/koellner_etal2004.pdf), but I could not quite understand the approach here.
I appreciate any suggestions.
Hello there,
Please see the following link
Best wishes
http://www.nature.com/ismej/journal/v1/n4/full/ismej200753a.html
Dear Bilgenur,
I found your question very interesting.
your difficulties could be solved using EstimateS. With this software, you could compare those different-effort samplings.
http://viceroy.eeb.uconn.edu/estimates/estimatespages/estimates.php
do you use any method to determine if your curves reached the asymptote?
Hello everyone !
I m getting issues in making rarefaction curve for my data . I want to have a graph similar to this paper (as below) and I am following the same protocol they mentioned in paper . They are using here the “specaccum” in the R package, vegan. But I was not able to get the same graph for eg. Y axis as SNPs , instead I am getting species diversity with different scale .
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https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045520#pone.0045520-Microsatellite1
Please help me out !
Thanks
Another example of a similar graph is as below....
Article Evolution and taxonomic classification of human papillomavir...
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