Update: I can see that you used the function Shannon from the package QSutils. This would supplement the iNext package I used and solve the problem. Thank you.
On Thu, Sep 10, 2020 at 10:35 AM Luigi Marongiu <marongiu.lu...@gmail.com> wrote: > > Thank you very much for the code, that was very helpful. > I got the article by Hutcheson -- I don't know if I can distribute it > , given the possible copyrights, or if I can attach it here -- but it > does not report numbers directly: it refers to a previous article > counting bird death on a telegraph each year. The numbers > are: > bird_1956 <- c(4,4,190,135,56,3,2,2,1,12,41,201,1,0,131,3) > bird_1957 <- c(4,111,53,66,146,222,126,61,0,2323,21) > bird_1958 <- c(0,3,32,228,56,102,0,11,2,220,0) > bird_1959 <- c(0,0,14,59,26,68,0) > bird_1960 <- c(0,0,73,66,71,25,0,109,63,1) > > This for sake of the argument. > As for my problem, I implemented the Shannon index with the package > iNext, which only gives me the index itself and the 95% CI. Even when > I implemented it with vegan, I only got the index. Essentially I don't > have a count of species I could feed into the Hutcheson's. Is there a > way to extract these data? Or to run a Hutcheson's on the final index? > Thank you > > On Tue, Sep 8, 2020 at 7:43 PM Karl Schilling > <karl.schill...@uni-bonn.de> wrote: > > > > Dear Luigi, > > > > below some code I cobbled together based on the Hutcheson paper you > > mentioned. I was lucky to find code to calculate h and, importantly, its > > variance in the R-package QSutils - you may find it on the Bioconductor > > website. > > > > here is the code, along with an example. I also attach the code as an > > R-file. > > > > Hope that helps. > > All my best > > > > Karl > > PS don't forget to adjust for multiple testing if you compare more than > > two groups. > > K > > > > > > # load package needed > > # QSutils is on Bioconductor > > library(QSutils) > > > > # here some exemplary data - these are the data from Pilou 1966 that are > > used > > # in the second example of Hutcheson, J theor Biol 129:151-154 (1970) > > > > earlier <- c(0,0,146,0,5,46,0,1,295,0,0,3,0,0,0,0,0) > > later <- c(0,0,142,0,5,46,0,1,246,0,0,3,0,0,0,0,0) > > # numbers of the first example used by Hutcheson were unfortunately not > > # available to me > > > > # here starts the code ; you may replace the variables "earlier" and "later" > > # by your own numbers. > > > > # calculate h, var(h) etc > > h1 <- Shannon(earlier) > > varh1 <- ShannonVar(earlier) > > n1 <- sum (earlier) > > h2 <- Shannon(later) > > varh2 <- ShannonVar(later) > > n2 <- sum (later) > > degfree <- (varh1 + varh2)**2 /(varh1**2/n1 + varh2**2 /n2) > > > > # compare numbers with those in the paper > > h1 > > h2 > > varh1 > > varh2 > > # I assume that minor numerical differences are due to differences in the > > # numerical precision of computers in the early seventies and today / KS > > > > # this is the actual t-test > > t <- (h1-h2) /sqrt(varh1 + varh2) > > p <- 2*pt(-abs(t),df= degfree) > > p > > > > # that's it > > # Best > > # Karl > > -- > > Karl Schilling, MD > > Professor of Anatomy and Cell Biology > > Anatomisches Institut > > Rheinische Friedrich-Wilhelms-Universität > > Nussallee 10 > > > > D-53115 Bonn > > Germany > > > > phone ++49-228-73-2602 > > > > > -- > Best regards, > Luigi -- Best regards, Luigi ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.