On 17 October 2014 06:44, Bob O'Hara <[email protected]> wrote: > On 17/10/14 13:54, "José M. Blanco Moreno" wrote: > >> Dear users >> >> I have been checking the values returned by the function estimateR >> against the formulae in the appendix to nonparametric estimators of >> species richness in EstimateS >> (http://viceroy.eeb.uconn.edu/EstimateS/EstimateSPages/EstSUsersGuide/ >> EstimateSUsersGuide.htm#AppendixB)... >> and they do not match each other. >> >> Where does this line of code in vegan:::estimateR.default come from? >> >> sd.Chao1 <- sqrt(a[2] * ((G^4)/4 + G^3 + (G^2)/2)) >> >> It is from any other reference that I should have under control? >> >> Unless Jari added something, the functions come from my paper from about > 10 years ago: > O’Hara RB (2005) Species richness estimators: how many species can dance > on the head of a pin? J Anim Ecol 74: 375–386. > http://doi.wiley.com/10.1111/j.1365-2656.2005.00940.x, which refers to > Chao (1987), which is cited in the estimateR documentation. EstimateS now > uses a small sample correction: <http://viceroy.eeb.uconn.edu/ > EstimateS/EstimateSPages/EstSUsersGuide/EstimateSUsersGuide.htm# > Chao1AndChao2> > Does this account for the discrepancy? > > Bob >
Yep, vegan does not include the small sample correction. The Chao1 computation is here: https://github.com/vegandevs/vegan/blob/master/R/estimateR.default.R#L44 but we can certainly add it if this is useful? (And I suppose it is if EstimateS has included it by default now...) G > -- > > Bob O'Hara > > Biodiversity and Climate Research Centre > Senckenberganlage 25 > D-60325 Frankfurt am Main, > Germany > > Tel: +49 69 7542 1863 > Mobile: +49 1515 888 5440 > WWW: http://www.bik-f.de/root/index.php?page_id=219 > Blog: http://blogs.nature.com/boboh > Journal of Negative Results - EEB: www.jnr-eeb.org > > > _______________________________________________ > R-sig-ecology mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-ecology > -- Gavin Simpson, PhD [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
