EstimateR and Chao 1 standard deviation
On 17/10/14 13:54, "Jos? 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
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