Why do you want to do this? Why not simply use Fisher's exact test? N <- 2178 N1 <- 165 N2 <- 331 J <- 97 ct <- rbind(c(J, N1-J), c(N2-J, N-N1-N2+J)) fisher.test(ct)
Background explanation: - Your formula computes the log hypergeometric probability for a contingency table as ct above, but with k instead of J. - It does so in an unnecessarily complicated way: three terms would be enough (cf. the equation at http://www.collocations.de/AM/section3.html; with C1=N1, C2=N-C1, R1=N2). - If you want to test for a positive association between the two animals, you should be adding up the probabilities for k >= J to obtain a p-value, rather than k <= J (what would this sum of probabilities tell you?). - lpvec doesn't contain probabilities, but log probabilities. What sense would there be in adding those up? In any case, you should obtain a negative value because all the individual logs are negative. Best, Stefan > On 25 Jun 2016, at 16:13, Gonçalo Ferraz <gferra...@gmail.com> wrote: > > I am working on interactions between animals, studying whether animal 1 is > attracted to animal 2 (or vice-versa). I looked for the two animals in N=2178 > sampling occasions, finding animal 1 a total of N1=165 times, and animal 2 a > total of N2=331 times. In J=97 occasions, I saw both animals at the same > time. > > The more frequently I see the two animals in the same sampling occasion, the > more I will believe that they are attracted to each other. Therefore, I want > to calculate the probability of finding J<=97 when the two animals are moving > around independently of each other. The higher this probability, the stronger > the attraction. > > Following Veech (Journal of Biogeography 2014, 41: 1029-1035) I compute the > log probability of obtaining a number n of encounters between animals as > ‘lpn’ in the function lveech: > ______________________________________________ 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.
