[R] Some code to run Hutcheson t-test using R

[Luigi Marongiu]

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.luigi using 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.schilling using 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