On 17 October 2014 10:04, Bob O'Hara <[email protected]> wrote: > On 10/17/2014 05:36 PM, Gavin Simpson wrote: > > 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...) > > Might as well. it looks like it shouldn't make a huge difference > unless sample sizes are small. > > Bob >
Okay, I'll see about getting this into vegan 2.2-0 which is about ready for release in the next couple of weeks. Cheers G > 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 > > > > -- > 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 > > -- Gavin Simpson, PhD [[alternative HTML version deleted]] _______________________________________________ R-sig-ecology mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
