Hello all, I want to calculate classic diversity indexes from my zooplankton samples. The problem is that the number of individuals is not the same in all cases (some samples were semi-empty) and that is the case for the amount of sample I analysed. In order to standardise for effort, I want to do the following: a) randomly sample e.g. 50 individuals from each of my sample, so that I standardise for effort (that's the difficult part) b) then calculate on this newly created matrix all the typical indexes (that's the easy part) I ll give an example of a dataset in R, where samples are rows and species are columns: 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 45 5 57 0 0 0 0 0 0 0 13 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 3 0 0 12 8 0 57 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 105 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 100 0 0 0 35 0 55 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 34 21 0 0 0 0 0 0 0 0 9 17 0 0 0 0 54 0 0 0 27 5 0 0 0 0 1 0 0 0 1 0 0 0 0 0 17 0 0 0 54 3 0 0 0 1 0 0 1 0 6 10 0 0 0 1 18 0 0 0 1 2 0 6 2 0 5 0 0 0 35 57 0 0 0 0 3 0 0 0 4 3 0 0 0 0 0 0 0 0 6 5 0 0 0 0 0 0 0 0 5 4 0 0 0 10 5 8 10 0 25 19 0 0 0 0 2 7 0 0 6 11 0 0 0 15 0 0 0 0 8 7 0 0 0 13 2 0 0 0 20 11 0 0 0 13 0 0 0 0 0 11 0 0 0 8 0 0 0 0 15 10 0 0 0 0 1 0 32 1 13 12 0 0 0 Anybody any ideas how to do this in R? -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Diversity-on-standardised-densities-in-R-tp7578474.html Sent from the r-sig-ecology mailing list archive at Nabble.com.
Diversity on standardised densities in R
8 messages · Vít Syrovátka, Mario José Marques, Peter Solymos +1 more
By the way, I think I could use (if Zoop tha name of the dataset) rrarefy(Zoop, sample=50). However, in this case it will not allow me since there are samples with zero individuals. Even if I delete those, there will be some with less than 50 indiv. But I would prefer to standardise effort for 50 individuals. This function, or at least in this form, does not allow that. -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Diversity-on-standardised-densities-in-R-tp7578474p7578475.html Sent from the r-sig-ecology mailing list archive at Nabble.com.
Hi, vegan::rrarefy() is the right way to do this. However, I can't imagine, how to take 50 random individuals from a sample with less then 50 individuals. One doesn't know, what species would be collected in case of a larger sampling effort, R doesn't know either. I would suggest doing this only for samples with more individuals, or taking a smaller number of individuals. Hope that helps, Vit Dne 2013-10-24 21:08, Paris napsal:
By the way, I think I could use (if Zoop tha name of the dataset) rrarefy(Zoop, sample=50). However, in this case it will not allow me since there are samples with zero individuals. Even if I delete those, there will be some with less than 50 indiv. But I would prefer to standardise effort for 50 individuals. This function, or at least in this form, does not allow that. -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Diversity-on-standardised-densities-in-R-tp7578474p7578475.html Sent from the r-sig-ecology mailing list archive at Nabble.com.
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Hi Paris, excuse-me if I do not understand you. I think that or you standardize you effort to less individual in your samples or you extrapolation your sample to that more abundant. If you have sample with less individual, like you say, it is not recomended to do extrapolation. If your accumulation curves, for each sample, reaches asymptote, I think that you can compare communities without standardize. For zooplancton, maybe is possible to reaches asymptote. I hope have helped you. Best regards, Mario ................................................... Doctoral student in Ecology Institute of Biology, Dept. Plant Biology, Ecology Lab. State University of Campinas - UNICAMP Campinas, S?o Paulo, Brazil
On 24-10-2013 16:45, Paris wrote:
Hello all, I want to calculate classic diversity indexes from my zooplankton samples. The problem is that the number of individuals is not the same in all cases (some samples were semi-empty) and that is the case for the amount of sample I analysed. In order to standardise for effort, I want to do the following: a) randomly sample e.g. 50 individuals from each of my sample, so that I standardise for effort (that's the difficult part) b) then calculate on this newly created matrix all the typical indexes (that's the easy part) I ll give an example of a dataset in R, where samples are rows and species are columns: 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 85 0 0 0 0 0 0 0 45 5 57 0 0 0 0 0 0 0 13 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 3 0 0 12 8 0 57 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 59 0 0 0 0 0 0 0 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 105 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 100 0 0 0 35 0 55 0 0 0 0 0 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 34 21 0 0 0 0 0 0 0 0 9 17 0 0 0 0 54 0 0 0 27 5 0 0 0 0 1 0 0 0 1 0 0 0 0 0 17 0 0 0 54 3 0 0 0 1 0 0 1 0 6 10 0 0 0 1 18 0 0 0 1 2 0 6 2 0 5 0 0 0 35 57 0 0 0 0 3 0 0 0 4 3 0 0 0 0 0 0 0 0 6 5 0 0 0 0 0 0 0 0 5 4 0 0 0 10 5 8 10 0 25 19 0 0 0 0 2 7 0 0 6 11 0 0 0 15 0 0 0 0 8 7 0 0 0 13 2 0 0 0 20 11 0 0 0 13 0 0 0 0 0 11 0 0 0 8 0 0 0 0 15 10 0 0 0 0 1 0 32 1 13 12 0 0 0 Anybody any ideas how to do this in R? -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Diversity-on-standardised-densities-in-R-tp7578474.html Sent from the r-sig-ecology mailing list archive at Nabble.com.
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2 days later
Hi thanks for your comment. Thought the same, but was worth trying if there is an alternative! -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Diversity-on-standardised-densities-in-R-tp7578474p7578480.html Sent from the r-sig-ecology mailing list archive at Nabble.com.
Hello Mario, the only reason I was trying to do this unorthodox method, is because I know that the abundances I have will give more or less biased diversity calculations and I was trying to get around that. However, it might be good to mention that in the discussion anyway, and compare the extrapolated diversity as suggested. -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Diversity-on-standardised-densities-in-R-tp7578474p7578481.html Sent from the r-sig-ecology mailing list archive at Nabble.com.
Hello Peter, will try it your way in R and see what results I ll get. Thanks -- View this message in context: http://r-sig-ecology.471788.n2.nabble.com/Diversity-on-standardised-densities-in-R-tp7578474p7578482.html Sent from the r-sig-ecology mailing list archive at Nabble.com.